Structure and function of photosystem I: interaction with its soluble electron carriers and external antenna systems

Identification of two recessive etiolation genes (py1, py2) in pakchoi (Brassica rapa L. ssp. chinensis)

BACKGROUND

Leaf color is a major agronomic trait, which has a strong influence on crop yields. Isolating leaf color mutants can represent valuable materials for research in chlorophyll (Chl) biosynthesis and metabolism regulation.

RESULTS

In this study, we identified a stably inherited yellow leaf mutant derived from 'Huaguan' pakchoi variety via isolated microspore culture and designated as pylm. This mutant displayed yellow leaves after germination. Its etiolated phenotype was nonlethal and stable during the whole growth period. Its growth was weak and its hypocotyls were markedly elongated. Genetic analysis revealed that two recessive nuclear genes, named py1 and py2, are responsible for the etiolation phenotype. Bulked segregant RNA sequencing (BSR-Seq) showed that py1 and py2 were mapped on chromosomes A09 and A07, respectively. The genes were single Mendelian factors in F_3:4 populations based on a 3:1 phenotypic segregation ratio. The py1 was localized to a 258.3-kb interval on a 34-gene genome. The differentially expressed gene BraA09004189 was detected in the py1 mapping region and regulated heme catabolism. One single-nucleotide polymorphism (SNP) of BraA09004189 occurred in pylm. A candidate gene-specific SNP marker in 1520 F_3:4 yellow-colored individuals co-segregated with py1. For py2, 1860 recessive homozygous F_3:4 individuals were investigated and localized py2 to a 4.4-kb interval. Of the five genes in this region, BraA07001774 was predicted as a candidate for py2. It encoded an embryo defective 1187 and a phosphotransferase related to chlorophyll deficiency and hypocotyl elongation. One SNP of BraA07001774 occurred in pylm. It caused a single amino acid mutation from Asp to Asn. According to quantitative real-time polymerase chain reaction (qRT-PCR), BraA07001774 was downregulated in pylm.

CONCLUSIONS

Our study identified a Chl deficiency mutant pylm in pakchoi. Two recessive nuclear genes named py1 and py2 had a significant effect on etiolation. Candidate genes regulating etiolation were identified as BraA09004189 and BraA07001774, respectively. These findings will elucidate chlorophyll metabolism and the molecular mechanisms of the gene interactions controlling pakchoi etiolation.

Structural basis for energy and electron transfer of the photosystem I-IsiA-flavodoxin supercomplex

Under iron-deficiency stress, which occurs frequently in natural aquatic environments, cyanobacteria reduce the amount of iron-enriched proteins, including photosystem I (PSI) and ferredoxin (Fd), and upregulate the expression of iron-stress-induced proteins A and B (IsiA and flavodoxin (Fld)). Multiple IsiAs function as the peripheral antennae that encircle the PSI core, whereas Fld replaces Fd as the electron receptor of PSI. Here, we report the structures of the PSI₃-IsiA₁₈-Fld₃ and PSI₃-IsiA₁₈ supercomplexes from Synechococcus sp. PCC 7942, revealing features that are different from the previously reported PSI structures, and a sophisticated pigment network that involves previously unobserved pigment molecules. Spectroscopic results demonstrated that IsiAs are efficient light harvesters for PSI. Three Flds bind symmetrically to the trimeric PSI core-we reveal the detailed interaction and the electron transport path between PSI and Fld. Our results provide a structural basis for understanding the mechanisms of light harvesting, energy transfer and electron transport of cyanobacterial PSI under stressed conditions.

Comparative transcriptome analysis of Bambusa pervariabilis × Dendrocalamopsis grandis against Arthrinium phaeospermum under protein AP-toxin induction

Bambusapervariabilis × Dendrocalamopsisgrandis, a fast-growing and easily propagated bamboo species, has been extensively planted in the southern China, resulting in huge ecological benefits. In recent years, it was found that the pathogenic fungus Arthrinium phaeospermum caused the death of a large amount of bamboo. In this study, the transcriptome of B. pervariabilis × D. grandis, induced by inactivated protein AP-toxin from A. phaeospermum was sequenced and analyzed, to reveal the resistance mechanism induced by biotic agents of B. pervariabilis × D. grandis against A. phaeospermum at the gene level. Transcriptome sequencing was performed by Illumina HiSeq 2000 in order to analyze the differentially expressed genes (DEGs) of B. pervariabilis × D. grandis in response to different treatment conditions. In total, 201,875,606 clean reads were obtained, and the percentage of Q30 bases in each sample was more than 94.21%. There were 6398 DEGs in the D-J group (inoculation with a pathogenic spore suspension after three days of AP-toxin induction) compared to the S-J group (inoculation with a pathogenic spore suspension after inoculation of sterile water for three days) with 3297 up-regulated and 3101 down-regulated genes. For the D-S group (inoculation with sterile water after inoculation of AP-toxin for three days), there were 2032 DEGs in comparison to the S-S group (inoculation with sterile water only), with 1035 up-regulated genes and 997 down-regulated genes. These identified genes were mainly involved in lignin and phytoprotein synthesis, tetrapyrrole synthesis, redox reactions, photosynthesis, and other processes. The fluorescence quantitative results showed that 22 pairs of primer amplification products were up-regulated and 7 were down-regulated. The rate of similarity between these results and the sequencing results of the transcription group was 100%, which confirmed the authenticity of the transcriptome sequencing results. Redox proteins, phenylalanine ammonia lyase, and S-adenosine-L-methionine synthetase, among others, were highly expressed; these results may indicate the level of disease resistance of the bamboo. These results provide a foundation for the further exploration of resistance genes and their functions.

A lil3 chlp double mutant with exclusive accumulation of geranylgeranyl chlorophyll displays a lethal phenotype in rice

BACKGROUND

Phytyl residues are the common side chains of chlorophyll (Chl) and tocopherols. Geranylgeranyl reductase (GGR), which is encoded by CHLP gene, is responsible for phytyl biosynthesis. The light-harvesting like protein LIL3 was suggested to be required for stability of GGR and protochlorophyllide oxidoreductase in Arabidopsis.

RESULTS

In this study, we isolated a yellow-green leaf mutant, 637ys, in rice (Oryza sativa). The mutant accumulated majority of Chls with unsaturated geranylgeraniol side chains and displayed a yellow-green leaf phenotype through the whole growth period. The development of chloroplasts was suppressed, and the major agronomic traits, especially No. of productive panicles per plant and of spikelets per panicle, dramatically decreased in 637ys. Besides, the mutant exhibited to be sensitive to light intensity and deficiency of tocopherols without obvious alteration in tocotrienols in leaves and grains. Map-based cloning and complementation experiment demonstrated that a point mutation on the OsLIL3 gene accounted for the mutant phenotype of 637ys. OsLIL3 is mainly expressed in green tissues, and its encoded protein is targeted to the chloroplast. Furthermore, the 637ys 502ys (lil3 chlp) double mutant exclusively accumulated geranylgeranyl Chl and exhibited lethality at the three-leaf stage.

CONCLUSIONS

We identified the OsLIL3 gene through a map-based cloning approach. Meanwhile, we demonstrated that OsLIL3 is of extreme importance to the function of OsGGR, and that the complete replacement of phytyl side chain of chlorophyll by geranylgeranyl chain could be fatal to plant survival in rice.

Genetic analysis and fine mapping of a qualitative trait locus wpb1 for albino panicle branches in rice

Chloroplast plays an important role in the plant life cycle. However, the details of its development remain elusive in rice. In this study, we report the fine-mapping of a novel rice gene wpb1 (white panicle branch 1), which affects chloroplast biogenesis, from a tropical japonica variety that results in an albino panicle branches at and after the heading stage. The wpb1 variety was crossed with Nipponbare to generate the F₂ and BC₁F₂ populations. Green and white panicle branch phenotypes with a 3:1 segregation ratio was observed in the F₂ population. Bulked segregant analysis (BSA) based on whole genome resequencing was conducted to determine the wpb1 locus. A candidate interval spanning from 11.35 to 23.79M (physical position) on chromosome 1 was identified. The results of BSA analysis were verified by a 40K rice SNP-array using the BC₁F₂ population. A large-scale F₂ population was used to pinpoint wpb1, and the locus was further narrowed down to a 95-kb interval. Furthermore, our results showed that the expression levels of the majority of the genes involved in Chl biosynthesis, photosynthesis and chloroplast development were remarkably affected in wpb1 variety and in F₂ plants with a white panicle branch phenotype. In line with the results mentioned above, anatomical structural examination and chlorophyll (Chl) content measurement suggested that wpb1 might play an important role in the regulation of chloroplast development. Further cloning and functional characterization of the wpb1 gene will shed light on the molecular mechanism underlying chloroplast development in rice.

Function of the IsiA pigment-protein complex in vivo

The acclimation of cyanobacterial photosynthetic apparatus to iron deficiency is crucial for their performance under limiting conditions. In many cyanobacterial species, one of the major responses to iron deficiency is the induction of isiA. The function of the IsiA pigment-protein complex has been the subject of intensive research. In this study of the model Synechocystis sp. PCC 6803 strain, we probe the accumulation of the pigment-protein complex and its effects on in vivo photosynthetic performance. We provide evidence that in this organism the dominant factor controlling IsiA accumulation is the intracellular iron concentration and not photo-oxidative stress or redox poise. These findings support the use of IsiA as a tool for assessing iron bioavailability in environmental studies. We also present evidence demonstrating that the IsiA pigment-protein complex exerts only small effects on the performance of the reaction centers. We propose that its major function is as a storage depot able to hold up to 50% of the cellular chlorophyll content during transition into iron limitation. During recovery from iron limitation, chlorophyll is released from the complex and used for the reconstruction of photosystems. Therefore, the IsiA pigment-protein complex can play a critical role not only when cells transition into iron limitation, but also in supporting efficient recovery of the photosynthetic apparatus in the transition back out of the iron-limited state.

Tandem 13-Lipoxygenase Genes in a Cluster Confers Yellow-Green Leaf in Cucumber

Some lipoxygenase (LOX) isoenzymes can co-oxidize carotenoids. Carotenoids are collectors of light energy for photosynthesis and can protect plants from reactive oxygen species and coloration. This study isolated the cucumber (Cucumis sativus L.) yellow-green leaf mutant (ygl1), which had yellow-green leaves with decreased chlorophyll synthesis, increased relative carotenoid content, and delayed chloroplast development. Genetic analysis demonstrated that the phenotype of ygl1 was caused by a recessive mutation in a nuclear gene. The bulked segregants were resequenced, and the candidate ygl1 locus identified was mapped to the 9.2 kb region of the chromosome 4. Sequence analysis revealed that ygl1 encodes the tandem 13-LOX genes in a cluster. Four missense mutations were found in four tandem 13-LOX genes (Csa4M286960, Csa4M287550, Csa4M288070, and Csa4M288080) in the ygl1 mutant, and the four 13-LOX genes showed high similarity with one another. The transient RNA interference and virus-induced gene silencing of these genes simultaneously resulted in yellow-green leaves with a reduced amount of chloroplasts and increased relative carotenoid content, which were observed in the ygl1 mutant. This evidence supported the non-synonymous SNPs (Single Nucleotide Polymorphism) in the four tandem 13-LOX genes as being the causative mutation for the yellow-green leaves. Furthermore, this study provides a new allele for breeding cucumbers with yellow-green leaves and serves as an additional resource for studying carotenoid biosynthesis.

Comparative Proteomic Analysis Reveals That Chlorophyll Metabolism Contributes to Leaf Color Changes in Wucai ( Brassica campestris L.) Responding to Cold Acclimation

Chlorophyll is a vital photosynthetic pigment that plays a key role in plant development, participating in light energy capture and energy conversion. In this study, a novel wucai ( Brassica campestris L.) germplasm with green outer leaves and yellow inner leaves at the adult stage (W7-2) was used to examine chlorophyll metabolism response to cold acclimation. A green leaf wucai genotype without leaf color changes named W7-1 was selected as the control to evaluate the chlorophyll metabolism changes of W7-2. Compared to W7-1, the contents of chlorophyll a (Chl a) and chlorophyll b (Chl b) in W7-2 were significantly reduced at five developmental stages (13, 21, 29, 37, and 45 days after planting (DAP)). An iTRAQ-based quantitative proteomic analysis was carried out at 21 and 29 DAP according to the leaf color changes in both of genotypes. 1409 proteins were identified, while 218 of them displayed differential accumulations between W7-2 and W7-1 during the two developmental stages. The differentially expressed proteins (DEPs) mainly assigned to chlorophyll biosynthesis, photosynthesis, carbohydrate metabolism, ribosome metabolism and posttranslational modification. Among these DEPs, NADPH-protochlorophyllide oxidoreductase (PORB) and Mg-protoporphyrin IX chelatase 1 (CHLI1) were the key enzymes participating in chlorophyll (Chl) biosynthesis, which was down-regulated at 21 DAP and up-regulated at 29 DAP in W7-2 compared with W7-1, respectively. The expression analysis of genes of three subunits of Mg-chelatase ( CHLI1, CHLD, and CHLH), Genomes Uncoupled 4 ( GUN4), and Thioredoxin ( TRX3) associated with chlorophyll metabolism also displayed significant down-regulation in W7-2. In particular, PORB showed significant up-regulation in W7-2, significantly affecting chlorophyll biosynthesis. Additionally, differences in chlorophyll metabolism between W7-2 and W7-1 were in terms of altered photosynthesis, carbohydrate, and energy metabolism. We found that the transcription levels of most photosynthesis proteins showed significantly lower levels, and the genes expression level, associated with carbohydrate and energy metabolism, were lower in W7-2 than in W7-1. Therefore, the present study results help understand the physiological and molecular mechanisms underlying leaf coloring responding to cold acclimation.

Overexpression of CONSTANS-like 16 enhances chlorophyll accumulation in petunia corollas

We have previously found that a gene closely related to Arabidopsis CONSTANS-like 16 (COL16) was coordinately expressed with chlorophyll content in chrysanthemum petals and leaves. Here, to elucidate whether COL16 is involved in the regulation of chlorophyll biosynthesis and accumulation, we analyzed the function of COL16 in petunia (Petunia hybrida). We identified three petunia COL16 homologs: PhCOL16a, PhCOL16b, and PhCOL16c. Expression patterns of all three homologs were associated with chlorophyll content, with lower levels in white corollas than in pale green corollas, and relatively high levels in leaves. The result suggests that PhCOL16 homologs are involved in chlorophyll accumulation. We introduced a PhCOL16a overexpression construct into petunia. The transgenic plants had pale green corollas with a higher chlorophyll content than wild-type plants. Expression of genes encoding key enzymes of chlorophyll biosynthesis was significantly higher in the transgenic plants than in the wild-type plants. The results indicate that PhCOL16 positively regulates chlorophyll biosynthesis.

Map-Based Cloning and Functional Analysis of YE1 in Rice, Which Is Involved in Light-Dependent Chlorophyll Biogenesis and Photoperiodic Flowering Pathway

Light is one of the most important environmental factors that affect many aspects of plant growth, including chlorophyll (Chl) synthesis and flowering time. Here, we identified a rice mutant, yellow leaf and early flowering (ye1), and characterized the gene YE1 by using a map-based cloning method. YE1 encodes a heme oxygenase, which is localized to the chloroplasts. YE1 is expressed in various green tissues, especially in leaves, with a diurnal-rhythmic expression pattern, and its transcripts is also induced by light during leaf-greening. The mutant displays decreased Chl contents with less and disorderly thylakoid lamellar layers in chloroplasts, which reduced the photosynthesis rate. The early flowering phenotype of ye1 was not photoperiod-sensitive. Furthermore, the expression levels of Chl biosynthetic genes were downregulated in ye1 seedlings during de-etiolation responses to light. We also found that rhythmic expression patterns of genes involved in photoperiodic flowering were altered in the mutant. Based on these results, we infer that YE1 plays an important role in light-dependent Chl biogenesis as well as photoperiodic flowering pathway in rice.

Physiological and proteome studies of maize (Zea mays L.) in response to leaf removal under high plant density

BACKGROUND

Under high plant density, intensifying competition among individual plants led to overconsumption of energy and nutrients and resulted in an almost dark condition in the lower strata of the canopy, which suppressed the photosynthetic potential of the shaded leaves. Leaf removal could help to ameliorate this problem and increase crop yields. To reveal the mechanism of leaf removal in maize, tandem mass tags label-based quantitative analysis coupled with liquid chromatography-tandem mass spectrometry were used to capture the differential protein expression profiles of maize subjected to the removal of the two uppermost leaves (S₂), the four uppermost leaves (S₄), and with no leaf removal as control (S₀).

RESULTS

Excising leaves strengthened the light transmission rate of the canopy and increased the content of malondialdehyde, whereas decreased the activities of superoxide dismutase and peroxidase. Two leaves removal increased the photosynthetic capacity of ear leaves and the grain yield significantly, whereas S₄ decreased the yield markedly. Besides, 239 up-accumulated proteins and 99 down-accumulated proteins were identified between S₂ and S₀, which were strongly enriched into 30 and 23 functional groups; 71 increased proteins and 42 decreased proteins were identified between S₄ and S₀, which were strongly enriched into 22 and 23 functional groups, for increased and decreased proteins, respectively.

CONCLUSIONS

Different defoliation levels had contrastive effects on maize. The canopy light transmission rate was strengthened and proteins related to photosynthetic electron-transfer reaction were up-regulated significantly for treatment S₂, which improved the leaf photosynthetic capacity, and obtained a higher grain yield consequently. In contrast, S₄ decreased the grain yield and increased the expressions of proteins and genes associated with fatty acid metabolism. Besides, both S₂ and S₄ exaggerated the defensive response of maize in physiological and proteomic level. Although further studies are required, the results in our study provide new insights to the further improvement in maize grain yield by leaf removal.

Effect of elevated CO2 on the interaction between invasive thrips, Frankliniella occidentalis, and its host kidney bean, Phaseolus vulgaris

BACKGROUND

Elevated CO₂ can alter the leaf damage caused by insect herbivores. Frankliniella occidentalis (Pergande) is highly destructive invasive pest of crop production worldwide. To investigate how elevated CO₂ affects F. occidentalis fed with Phaseolus vulgaris and, in particular, the interaction between plant defense and thrips anti-defense, nutrient content and antioxidant enzyme activity of P. vulgaris were measured, as well as the detoxifying enzyme activity of adult thrips.

RESULTS

Elevated CO₂ increased the soluble sugar, soluble protein and free amino acid content in non thrip-infested plants, and decreased superoxide dismutase (SOD) and peroxidase (POD) activity in these plants. Feeding thrips reduced the nutrient content in plants, and increased their SOD, catalase and POD activity. Variations in nutrient content and antioxidant enzyme activity in plants showed an opposite tendency over thrip feeding time. After feeding, acetylcholinesterase, carboxylesterase, and mixed-function oxidase activity in thrips increased to counter the plant defenses. Greater thrip densities induced stronger plant defenses and, in turn, detoxifying enzyme levels in thrips increased over thrip numbers.

CONCLUSION

Our study revealed that F. occidentalis can induce not only an antioxidant-associated plant defense, but also detoxifying enzymes in thrips. Elevated CO₂ might both enhance plant defense against thrip attack, and increase thrip anti-defense against plant defenses. © 2018 Society of Chemical Industry.

Lipid profiles reveal different responses to brown planthopper infestation for pest susceptible and resistant rice plants

INTRODUCTION

Brown planthopper (BPH) is the most destructive insect pest for rice, causing major reductions in rice yield and large economic losses. More than 31 BPH-resistance genes have been located, and several of them have been isolated. Nevertheless, the metabolic mechanism related to BPH-resistance genes remain uncharacterized.

OBJECTIVES

To elucidate the resistance mechanism of the BPH-resistance gene Bph6 at the metabolic level, a Bph6-transgenic line R6 (BPH-resistant) and the wild-type Nipponbare (BPH-susceptible) were used to investigate their lipid profiles under control and BPH treatments.

METHODS

In conjunction with multivariate statistical analysis and quantitative real-time PCR, BPH-induced lipid changes in leaf blade and leaf sheath were investigated by GC-MS-based lipidomics.

RESULTS

Forty-five lipids were identified in leaf sheath extracts. Leaf sheath lipidomics analysis results show that BPH infestation induces significant differences in the lipid profiles of Nipponbare and R6. The levels of hexadecanoic acid, methyl ester, linoleic acid, methyl ester, linolenic acid, methyl ester, glycidyl palmitate, eicosanoic acid, methyl ester, docosanoic acid, methyl ester, beta-monolinolein, campesterol, beta-sitosterol, cycloartenol, phytol and phytyl acetate had undergone enormous changes after BPH feeding. These results illustrate that BPH feeding enhances sterol biosynthetic pathway in Nipponbare plants, and strengthens wax biosynthesis and phytol metabolism in R6 plants. The results of quantitative real-time PCR of 5 relevant genes were consistent with the changes in metabolic level. Forty-five lipids were identified in the leaf blade extracts. BPH infestation induces distinct changes in the lipid profiles of the leaf blade samples of Nipponbare and R6. Although the lipid changes in Nipponbare are more drastic, the changes within the two varieties are similar. Lipid profiles in leaf sheath brought out significant differences than in leaf blade within Nipponbare and R6. We propose that Bph6 mainly affects the levels of lipids in leaf sheath, and mediates resistance by deploying metabolic re-programming during BPH feeding.

CONCLUSION

The results indicate that wax biosynthesis, sterol biosynthetic pathway and phytol metabolism play vital roles in rice response to BPH infestation. This finding demonstrated that the combination of lipidomics and quantitative real-time PCR is an effective approach to elucidating the interactions between brown planthopper and rice mediated by resistance genes.

Improving biomass and starch accumulation of bioenergy crop duckweed (Landoltia punctata) by abscisic acid application

Duckweed is a valuable feedstock for bioethanol production due to its high biomass and starch accumulation. In our preliminary experiment, we found that abscisic acid (ABA) could simultaneously increase starch and biomass accumulation of duckweed, but the mechanisms are still unclear. The results showed that the biomass production of duckweed reached up to 59.70 and 63.93 g m⁻² in 6 days, respectively, with an increase of 7% (P < 0.05) compared to the control. The starch percentage increased from 2.29% up to 46.18% after 14 days of treatment, with a total of starch level 2.6-fold higher than that of the control. Moreover, the level of endogenous ABA, zeatin-riboside (ZR) and indole-3-acetic acid (IAA) increased, while gibberellins (GAs) decreased. Notably, ABA content in treated samples reached 336.5 mg/kg (fresh weight), which was 7.5-fold greater than that of the control. Importantly, the enzyme activities involved in starch biosynthesis increased while those catalyzing starch degradation decreased after ABA application. Taken together, these results indicated that ABA can promote biomass and starch accumulation by regulating endogenous hormone levels and the activity of starch metabolism related key enzymes. These results will provide an operable method for high starch accumulation in duckweed for biofuels production.

Ion and metabolite transport in the chloroplast of algae: lessons from land plants

Chloroplasts are endosymbiotic organelles and play crucial roles in energy supply and metabolism of eukaryotic photosynthetic organisms (algae and land plants). They harbor channels and transporters in the envelope and thylakoid membranes, mediating the exchange of ions and metabolites with the cytosol and the chloroplast stroma and between the different chloroplast subcompartments. In secondarily evolved algae, three or four envelope membranes surround the chloroplast, making more complex the exchange of ions and metabolites. Despite the importance of transport proteins for the optimal functioning of the chloroplast in algae, and that many land plant homologues have been predicted, experimental evidence and molecular characterization are missing in most cases. Here, we provide an overview of the current knowledge about ion and metabolite transport in the chloroplast from algae. The main aspects reviewed are localization and activity of the transport proteins from algae and/or of homologues from other organisms including land plants. Most chloroplast transporters were identified in the green alga Chlamydomonas reinhardtii, reside in the envelope and participate in carbon acquisition and metabolism. Only a few identified algal transporters are located in the thylakoid membrane and play role in ion transport. The presence of genes for putative transporters in green algae, red algae, diatoms, glaucophytes and cryptophytes is discussed, and roles in the chloroplast are suggested. A deep knowledge in this field is required because algae represent a potential source of biomass and valuable metabolites for industry, medicine and agriculture.

Unique organization of photosystem I-light-harvesting supercomplex revealed by cryo-EM from a red alga

Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic algae and higher plants, PSI consists of a core surrounded by variable species and numbers of light-harvesting complex (LHC)I proteins, forming a PSI-LHCI supercomplex. Here, we report cryo-EM structures of PSI-LHCR from the red alga Cyanidioschyzon merolae in two forms, one with three Lhcr subunits attached to the side, similar to that of higher plants, and the other with two additional Lhcr subunits attached to the opposite side, indicating an ancient form of PSI-LHCI. Furthermore, the red algal PSI core showed features of both cyanobacterial and higher plant PSI, suggesting an intermediate type during evolution from prokaryotes to eukaryotes. The structure of PsaO, existing in eukaryotic organisms, was identified in the PSI core and binds three chlorophylls a and may be important in harvesting energy and in mediating energy transfer from LHCII to the PSI core under state-2 conditions. Individual attaching sites of LHCRs with the core subunits were identified, and each Lhcr was found to contain 11 to 13 chlorophylls a and 5 zeaxanthins, which are apparently different from those of LHCs in plant PSI-LHCI. Together, our results reveal unique energy transfer pathways different from those of higher plant PSI-LHCI, its adaptation to the changing environment, and the possible changes of PSI-LHCI during evolution from prokaryotes to eukaryotes.

Cytological, physiological, and transcriptomic analyses of golden leaf coloration in Ginkgo biloba L

Ginkgo biloba is grown worldwide as an ornamental plant for its golden leaf color. However, the regulatory mechanism of leaf coloration in G. biloba remains unclear. Here, we compared G. biloba gold-colored mutant leaves and normal green leaves in cytological, physiological and transcriptomic terms. We found that chloroplasts of the mutant were fewer and smaller, and exhibited ruptured thylakoid membranes, indistinct stromal lamellae and irregularly arranged vesicles. Physiological experiments also showed that the mutant had a lower chlorophyll, lower flavonoid and higher carotenoid contents (especially lutein). We further used transcriptomic sequencing to identify 116 differentially expressed genes (DEGs) and 46 transcription factors (TFs) involved in chloroplast development, chlorophyll metabolism, pigment biosynthesis and photosynthesis. Among these, the chlorophyll biosynthesis-related PPO showed down-regulation, while chlorophyll degradation-related NYC/NOL had up-regulated expression in mutant leaves. Z-ISO, ZDS, and LCYE, which are involved in carotenoid biosynthesis were up-regulated. Quantitative real-time PCR (RT-qPCR) further confirmed the altered expression levels of these genes at three stages. The alteration of PPO and NYC/NOL gene expression might affect chlorophyll biosynthesis and promote degradation of chlorophyll b to chlorophyll a, while the up-regulated genes Z-ISO, ZDS and LCYE enhanced carotenoid accumulation. Consequently, changes in the ratio of carotenoids to chlorophylls were the main factors driving the golden leaf coloration in the mutant G. biloba.

Yellow-Leaf 1 encodes a magnesium-protoporphyrin IX monomethyl ester cyclase, involved in chlorophyll biosynthesis in rice (Oryza sativa L.)

Magnesium-protoporphyrin IX monomethyl ester cyclase (MPEC) catalyzes the conversion of MPME to divinyl protochlorophyllide (DVpchlide). This is an essential enzyme during chlorophyll (Chl) biosynthesis but details of its function in rice are still lacking. Here, we identified a novel rice mutant yellow-leaf 1 (yl-1), which showed decreased Chl accumulation, abnormal chloroplast ultrastructure and attenuated photosynthetic activity. Map-based cloning and over-expression analysis suggested that YL-1 encodes a subunit of MPEC. The YL-1 protein localizes in chloroplasts, and it is mainly expressed in green tissues, with greatest abundance in leaves and young panicles. Results of qRT-PCR showed that Chl biosynthesis upstream genes were highly expressed in the yl-1 mutant, while downstream genes were compromised, indicating that YL-1 plays a pivotal role in the Chl biosynthesis. Furthermore, the expression levels of photosynthesis and chloroplast development genes were also affected. RNA-seq results futher proved that numerous membrane-associated genes, including many plastid membrane-associated genes, have altered expression pattern in the yl-1 mutant, implying that YL-1 is required for plastid membrane stability. Thus, our study confirms a putative MPME cyclase as a novel key enzyme essential for Chl biosynthesis and chloroplast membrane stability in rice.

Hybrid weakness in a rice interspecific hybrid is nitrogen-dependent, and accompanied by changes in gene expression at both total transcript level and parental allele partitioning

Background

Hybrid weakness, a phenomenon opposite to heterosis, refers to inferior growth and development in a hybrid relative to its pure-line parents. Little attention has been paid to the phenomenological or mechanistic aspect of hybrid weakness, probably due to its rare occurrence.

Methodology/Principal findings

Here, using a set of interspecific triploid F1 hybrids between Oryza sativa, ssp. japonica (genome AA) and a tetraploid wild rice species, O. alta (genome, CCDD), we investigated the phenotypic and physiological differences between the F1 hybrids and their parents under normal and nitrogen-limiting conditions. We quantified the expression levels of 21 key genes involved in three important pathways pertinent to the assayed phenotypic and physiological traits by real-time qRT-PCR. Further, we assayed expression partitioning of parental alleles for eight genes in the F1 hybrids relative to the in silico “hybrids” (parental cDNA mixture) under both normal and N-limiting conditions by using locus-specific cDNA pyrosequencing.

Conclusions/Significance

We report that the F1 hybrids showed weakness in several phenotypic traits at the final seedling-stage compared with their corresponding mid-parent values (MPVs). Nine of the 21 studied genes showed contrasted expression levels between hybrids and parents (MPVs) under normal vs. N-limiting conditions. Interestingly, under N-limiting conditions, the overtly enhanced partitioning of maternal allele expression in the hybrids for eight assayed genes echo their attenuated hybrid weakness in phenotypes, an observation further bolstered by more resemblance of hybrids to the maternal parent under N-limiting conditions compared to normal conditions in a suite of measured physiological traits. Our observations suggest that both overall expression level and differential partitioning of parental alleles of critical genes contribute to condition-specific hybrid weakness.

In vitro kinetics of P700+ reduction of Thermosynechococcus elongatus trimeric Photosystem I complexes by recombinant cytochrome c 6 using a Joliot-type LED spectrophotometer

The reduction rate of photo-oxidized Photosystem I (PSI) with various natural and artificial electron donors have been well studied by transient absorption spectroscopy. The electron transfer rate from various donors to P₇₀₀⁺ has been measured for a wide range of photosynthetic organisms encompassing cyanobacteria, algae, and plants. PSI can be a limiting component due to tedious extraction and purification methods required for this membrane protein. In this report, we have determined the in vivo, intracellular cytochrome c ₆ (cyt c ₆)/PSI ratio in Thermosynechococcus elongatus (T.e.) using quantitative Western blot analysis. This information permitted the determination of P₇₀₀⁺ reduction kinetics via recombinant cyt c ₆ in a physiologically relevant ratio (cyt c ₆: PSI) with a Joliot-type, LED-driven, pump-probe spectrophotometer. Dilute PSI samples were tested under varying cyt c ₆ concentration, temperature, pH, and ionic strength, each of which shows similar trends to the reported literature utilizing much higher PSI concentrations with laser-based spectrophotometer. Our results do however indicate kinetic differences between actinic light sources (laser vs. LED), and we have attempted to resolve these effects by varying our LED light intensity and duration. The standardized configuration of this spectrophotometer will also allow a more uniform kinetic analysis of samples in different laboratories. We can conclude that our findings from the LED-based system display an added total protein concentration effect due to multiple turnover events of P₇₀₀⁺ reduction by cyt c ₆ during the longer illumination regime.

Impaired Magnesium Protoporphyrin IX Methyltransferase (ChlM) Impedes Chlorophyll Synthesis and Plant Growth in Rice

Magnesium protoporphyrin IX methyltransferase (ChlM) catalyzes the formation of magnesium protoporphyrin IX monomethylester (MgPME) from magnesium protoporphyrin IX (MgP) in the chlorophyll synthesis pathway. However, no ChlM gene has yet been identified and studied in monocotyledonous plants. In this study, a spontaneous mutant, yellow-green leaf 18 (ygl18), was isolated from rice (Oryza sativa). This mutant showed yellow-green leaves, decreased chlorophyll level, and climate-dependent growth differences. Map-based cloning of this mutant identified the YGL18 gene LOC_Os06g04150. YGL18 is expressed in green tissues, especially in leaf organs, where it functions in chloroplasts. YGL18 showed an amino-acid sequence similarity to that of ChlM from different photosynthetic organisms. In vitro enzymatic assays demonstrated that YGL18 performed ChlM enzymatic activity, but ygl18 had nearly lost all ChlM activity. Correspondingly, the substrate MgP was largely accumulated while the product MgPME was reduced in ygl18 leaves. YGL18 is required for light-dependent and photoperiod-regulated chlorophyll synthesis. The retarded growth of ygl18 mutant plants was caused by the high light intensity. Moreover, the higher light intensity and longer exposure in high light intensity even made the ygl18 plants be more susceptible to death. Based on these results, it is suggested that YGL18 plays essential roles in light-related chlorophyll synthesis and light intensity-involved plant growth.

Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome

Background

Despite their versatile functions in multimeric protein complexes, in the modification of enzymatic activities, intercellular communication or regulatory processes, proteins shorter than 80 amino acids (μ-proteins) are a systematically underestimated class of gene products in bacteria. Photosynthetic cyanobacteria provide a paradigm for small protein functions due to extensive work on the photosynthetic apparatus that led to the functional characterization of 19 small proteins of less than 50 amino acids. In analogy, previously unstudied small ORFs with similar degrees of conservation might encode small proteins of high relevance also in other functional contexts.

Results

Here we used comparative transcriptomic information available for two model cyanobacteria, Synechocystis sp. PCC 6803 and Synechocystis sp. PCC 6714 for the prediction of small ORFs. We found 293 transcriptional units containing candidate small ORFs ≤80 codons in Synechocystis sp. PCC 6803, also including the known mRNAs encoding small proteins of the photosynthetic apparatus. From these transcriptional units, 146 are shared between the two strains, 42 are shared with the higher plant Arabidopsis thaliana and 25 with E. coli. To verify the existence of the respective μ-proteins in vivo, we selected five genes as examples to which a FLAG tag sequence was added and re-introduced them into Synechocystis sp. PCC 6803. These were the previously annotated gene ssr1169, two newly defined genes norf1 and norf4, as well as nsiR6(nitrogen stress-induced RNA 6) and hliR1(high light-inducible RNA 1) , which originally were considered non-coding. Upon activation of expression via the Cu^2+.responsive petE promoter or from the native promoters, all five proteins were detected in Western blot experiments.

Conclusions

The distribution and conservation of these five genes as well as their regulation of expression and the physico-chemical properties of the encoded proteins underline the likely great bandwidth of small protein functions in bacteria and makes them attractive candidates for functional studies.

Soybean proteins GmTic110 and GmPsbP are crucial for chloroplast development and function

We have identified a viable-yellow and a lethal-yellow chlorophyll-deficient mutant in soybean. Segregation patterns suggested single-gene recessive inheritance for each mutant. The viable- and lethal-yellow plants showed significant reduction of chlorophyll a and b. Photochemical energy conversion efficiency and photochemical reflectance index were reduced in the viable-yellow plants relative to the wildtype, whereas the lethal-yellow plants showed no electron transport activity. The viable-yellow plants displayed reduced thylakoid stacking, while the lethal-yellow plants exhibited failure of proplastid differentiation into normal chloroplasts with grana. Genetic analysis revealed recessive epistatic interaction between the viable- and the lethal-yellow genes. The viable-yellow gene was mapped to a 58kb region on chromosome 2 that contained seven predicted genes. A frame shift mutation, due to a single base deletion in Glyma.02g233700, resulted in an early stop codon. Glyma.02g233700 encodes a translocon in the inner membrane of chloroplast (GmTic110) that plays a critical role in plastid biogenesis. The lethal-yellow gene was mapped to an 83kb region on chromosome 3 that contained 13 predicted genes. Based on the annotated functions, we sequenced three potential candidate genes. A single base insertion in the second exon of Glyma.03G230300 resulted in a truncated protein. Glyma.03G230300 encodes for GmPsbP, an extrinsic protein of Photosystem II that is critical for oxygen evolution during photosynthesis. GmTic110 and GmPsbP displayed highly reduced expression in the viable- and lethal-yellow mutants, respectively. The yellow phenotypes in the viable- and lethal-yellow mutants were due to the loss of function of GmTic110 or GmPsbP resulting in photooxidative stress.

Comparative Proteomic and Physiological Analysis Reveals the Variation Mechanisms of Leaf Coloration and Carbon Fixation in a Xantha Mutant of Ginkgo biloba L

Yellow-green leaf mutants are common in higher plants, and these non-lethal chlorophyll-deficient mutants are ideal materials for research on photosynthesis and plant development. A novel xantha mutant of Ginkgo biloba displaying yellow-colour leaves (YL) and green-colour leaves (GL) was identified in this study. The chlorophyll content of YL was remarkably lower than that in GL. The chloroplast ultrastructure revealed that YL had less dense thylakoid lamellae, a looser structure and fewer starch grains than GL. Analysis of the photosynthetic characteristics revealed that YL had decreased photosynthetic activity with significantly high nonphotochemical quenching. To explain these phenomena, we analysed the proteomic differences in leaves and chloroplasts between YL and GL of ginkgo using two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF MS. In total, 89 differential proteins were successfully identified, 82 of which were assigned functions in nine metabolic pathways and cellular processes. Among them, proteins involved in photosynthesis, carbon fixation in photosynthetic organisms, carbohydrate/energy metabolism, amino acid metabolism, and protein metabolism were greatly enriched, indicating a good correlation between differentially accumulated proteins and physiological changes in leaves. The identifications of these differentially accumulated proteins indicates the presence of a specific different metabolic network in YL and suggests that YL possess slower chloroplast development, weaker photosynthesis, and a less abundant energy supply than GL. These studies provide insights into the mechanism of molecular regulation of leaf colour variation in YL mutants.

Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2

Small diffusible redox proteins facilitate electron transfer in respiration and photosynthesis by alternately binding to their redox partners and integral membrane proteins and exchanging electrons. Diffusive search, recognition, binding, and unbinding of these proteins often amount to kinetic bottlenecks in cellular energy conversion, but despite the availability of structures and intense study, the physical mechanisms controlling redox partner interactions remain largely unknown. The present molecular dynamics study provides an all-atom description of the cytochrome c2-docked bc1 complex in Rhodobacter sphaeroides in terms of an ensemble of favorable docking conformations and reveals an intricate series of conformational changes that allow cytochrome c2 to recognize the bc1 complex and bind or unbind in a redox state-dependent manner. In particular, the role of electron transfer in triggering a molecular switch and in altering water-mediated interface mobility, thereby strengthening and weakening complex formation, is described. The results resolve long-standing discrepancies between structural and functional data.

Physiological and Proteomic Responses of Continuous Cultures of Microcystis aeruginosa PCC 7806 to Changes in Iron Bioavailability and Growth Rate

The hepatotoxin microcystin (MCYST) is produced by a variety of freshwater cyanobacterial species, including Microcystis aeruginosa Interestingly, MCYST-producing M. aeruginosa strains have been shown to outcompete their nontoxic counterparts under iron-limiting conditions. However, the reasons for this are unclear. Here we examined the proteomic response of M. aeruginosa PCC 7806 continuous cultures under different iron and growth regimes. Iron limitation was correlated with a global reduction in levels of proteins associated with energy metabolism and photosynthesis. These proteomic changes were consistent with physiological observations, including reduced chlorophyll a content and reduced cell size. While levels of MCYST biosynthesis proteins did not fluctuate during the study period, both intra- and extracellular toxin quotas were significantly higher under iron-limiting conditions. Our results support the hypothesis that intracellular MCYST plays a role in protecting the cell against oxidative stress. Further, we propose that extracellular MCYST may act as a signaling molecule, stimulating MCYST production under conditions of iron limitation and enhancing the fitness of bloom populations.

IMPORTANCE

Microcystin production in water supply reservoirs is a global public health problem. Understanding the ecophysiology of hepatotoxic cyanobacteria, including their responses to the presence of key micronutrient metals such as iron, is central to managing harmful blooms. To our knowledge, this was the first study to examine proteomic and physiological changes occurring in M. aeruginosa continuous cultures under conditions of iron limitation at different growth rates.

Identification of a peroxisomal-targeted aldolase involved in chlorophyll biosynthesis and sugar metabolism in rice

Chlorophyll plays remarkable and critical roles in photosynthetic light-harvesting, energy transduction and plant development. In this study, we identified a rice Chl-deficient mutant, ygdl-1 (yellow green and droopy leaf-1), which showed yellow-green leaves throughout plant development with decreased content of Chls and carotene and an increased Chl a/b ratio. The ygdl-1 mutant also exhibited severe defects in chloroplast development, including disorganized grana stacks. Sequence analysis revealed that the mutant contained a T-DNA insertion within the promoter of a fructose-1,6-bisphosphate aldolase (OsAld-Y), which dramatically reduced the OsAld-Y mRNA level, and its identity was verified by transgenic complementation. Real-time PCR analysis showed that the expression levels of genes associated with chlorophyll biosynthesis and chloroplast development were concurrently altered in the ygdl-1 mutant. The expression of OsAld-Y-GFP fusion protein in tobacco epidermal cells showed that OsAld-Y was localized to the peroxisome. In addition, the analysis of primary carbon metabolites revealed the significantly reduced levels of sucrose and fructose in the mutant leaves, while the glucose content was similar to wild-type plants. Our results suggest that the OsAld-Y participates in Chl accumulation, chloroplast development and plant growth by influencing the photosynthetic rate of leaves and the sugar metabolism of rice.

Map-based cloning and functional analysis of YGL8, which controls leaf colour in rice (Oryza sativa)

BACKGROUND

As the indispensable part of plant, leaf blade mainly functions as the production workshops where organic substance is produced by photosynthesis. Leaf colour mutation is a genetic phenomenon that has a high frequency and is easily identified. The mutations always exhibit negative impact on the development of plants in any of the different stages of growth. Up to now, numerous genes involved in leaf colour mutations have been cloned.

RESULTS

In this study, a yellow-green leaf mutant, yellow-green leaf 8 (ygl8), with stable genetic phenotype, has been screened out in the progeny of an excellent indica restorer line Jinhui 10 with seeds treated by EMS. The levels of Chl a, Chl b and total chlorophyll were significantly lower in ygl8 than those in the WT throughout the whole growth period, while no clear change was noted in the Chl a/b ratio. Transmission electron microscopy demonstrated that the lamellae were clearly intumescent and intricately stacked in ygl8. Furthermore, compared with those of the WT, the stomatal conductance, intercellular CO2 concentration, photosynthetic rate and transpiration rate of ylg8 were all significantly lower. Map-based cloning results showed that Loc_Os01g73450, encoding a chloroplast-targeted UMP kinase, corresponded to Ygl8 and played an important role in regulating leaf colour in rice (Oryza sativa). Complementation of ygl8 with the WT DNA sequence of Loc_Os01g73450 led to restoration of the normal phenotype, and transgenic RNA interference plants showed a yellow-green colour. Analysis of the spatial and temporal expression of Ygl8 indicated that it was highly expressed in leaf blades and weakly expressed in other tissues. qRT-PCR also showed that the expression levels of the major Photosystem I core subunits plastome-encoded PsaA, PsaB and PsbC were significantly reduced in ygl8. The expression levels of nuclear-encoded gene involved in Chl biosynthesis HEMC, HEME, and PORA were also decreased when compared with the wild-type.

CONCLUSIONS

Independent of Chl biosynthesis and photosystem, YGL8 may affect the structure and function of chloroplasts grana lamellae by regulating plastid genome encoded thylakoid membrane constitutive gene expression and indirectly influences Chl biosynthesis.

PGL, encoding chlorophyllide a oxygenase 1, impacts leaf senescence and indirectly affects grain yield and quality in rice

Chlorophyll (Chl) b is a ubiquitous accessory pigment in land plants, green algae, and prochlorophytes. This pigment is synthesized from Chl a by chlorophyllide a oxygenase and plays a key role in adaptation to various environments. This study characterizes a rice mutant, pale green leaf (pgl), and isolates the gene PGL by using a map-based cloning approach. PGL, encoding chlorophyllide a oxygenase 1, is mainly expressed in the chlorenchyma and activated in the light-dependent Chl synthesis process. Compared with wild-type plants, pgl exhibits a lower Chl content with a reduced and disorderly thylakoid ultrastructure, which decreases the photosynthesis rate and results in reduced grain yield and quality. In addition, pgl exhibits premature senescence in both natural and dark-induced conditions and more severe Chl degradation and reactive oxygen species accumulation than does the wild-type. Moreover, pgl is sensitive to heat stress.

Iron-Nutrient Interactions within Phytoplankton

Iron limits photosynthetic activity in up to one third of the world's oceans and in many fresh water environments. When studying the effects of Fe limitation on phytoplankton or their adaptation to low Fe environments, we must take into account the numerous cellular processes within which this micronutrient plays a central role. Due to its flexible redox chemistry, Fe is indispensable in enzymatic catalysis and electron transfer reactions and is therefore closely linked to the acquisition, assimilation and utilization of essential resources. Iron limitation will therefore influence a wide range of metabolic pathways within phytoplankton, most prominently photosynthesis. In this review, we map out four well-studied interactions between Fe and essential resources: nitrogen, manganese, copper and light. Data was compiled from both field and laboratory studies to shed light on larger scale questions such as the connection between metabolic pathways and ambient iron levels and the biogeographical distribution of phytoplankton species.

Uniconazole-induced starch accumulation in the bioenergy crop duckweed (Landoltia punctata) I: transcriptome analysis of the effects of uniconazole on chlorophyll and endogenous hormone biosynthesis

BACKGROUND

Duckweed is a novel aquatic bioenergy crop that is found ubiquitously throughout the world. Uniconazole plays an important role in improving crop production through the regulation of endogenous hormone levels. We found that a high quantity and quality of duckweed growth can be achieved by uniconazole application, although the mechanisms are unknown.

RESULTS

The fronds of Landoltia punctata were sprayed evenly with 800 mg/L uniconazole. The dry weight following treatment increased by 10% compared to the controls at 240 h. Endogenous cytokinin (CK) and abscisic acid (ABA) content both increased compared to the control, while the level of gibberellins (GAs) decreased. Additionally, gene expression profiling results showed that the expression of transcripts encoding key enzymes involved in endogenous CK and ABA biosynthesis were up-regulated, while the transcripts of key enzymes for GAs biosynthesis were down-regulated. On the other hand, chlorophyll a and chlorophyll b contents were both increased compared with the control. Moreover, the net photosynthetic rate was elevated to 25.6 μmol CO2/m(2)/s compared with the control value of 22.05 μmol CO2/m(2)/s. Importantly, the expression of some chlorophyll biosynthesis-related transcripts was up-regulated.

CONCLUSION

Uniconazole treatment altered endogenous hormone levels and enhanced chlorophyll content and net photosynthetic rate in duckweed by regulating key enzymes involved in endogenous hormone and chlorophyll biosynthesis. The alterations of endogenous hormones and the increase of chlorophyll and photosynthetic rate data support the increase of biomass and starch accumulation.

Photoelectrochemistry of photosystem I bound in nafion

Developing a solid state Photosystem I (PSI) modified electrode is attractive for photoelectrochemical applications because of the quantum yield of PSI, which approaches unity in the visible spectrum. Electrodes are constructed using a Nafion film to encapsulate PSI as well as the hole-scavenging redox mediator Os(bpy)2Cl2. The photoactive electrodes generate photocurrents of 4 μA/cm(2) when illuminated with 1.4 mW/cm(2) of 676 nm band-pass filtered light. Methyl viologen (MV(2+)) is present in the electrolyte to scavenge photoelectrons from PSI in the Nafion film and transport charges to the counter electrode. Because MV(2+) is positively charged in both reduced and oxidized states, it is able to diffuse through the cation permeable channels of Nafion. Photocurrent is produced when the working electrode is set to voltages negative of the Os(3+)/Os(2+) redox potential. Charge transfer through the Nafion film and photohole scavenging at the PSI luminal surface by Os(bpy)2Cl2 depends on the reduction of Os redox centers to Os(2+) via hole scavenging from PSI. The optimal film densities of Nafion (10 μg/cm(2) Nafion) and PSI (100 μg/cm(2) PSI) are determined to provide the highest photocurrents. These optimal film densities force films to be thin to allow the majority of PSI to have productive electrical contact with the backing electrode.

All-atom molecular dynamics simulation of a photosystem i/detergent complex

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

A thylakoid membrane protein harboring a DnaJ-type zinc finger domain is required for photosystem I accumulation in plants

Photosystem I (PSI) is a large pigment-protein complex and one of the two photosystems that drive electron transfer in oxygenic photosynthesis. We identified a nuclear gene required specifically for the accumulation of PSI in a forward genetic analysis of chloroplast biogenesis in maize. This gene, designated psa2, belongs to the "GreenCut" gene set, a group of genes found in green algae and plants but not in non-photosynthetic organisms. Disruption of the psa2 ortholog in Arabidopsis likewise resulted in the specific loss of PSI proteins. PSA2 harbors a conserved domain found in DnaJ chaperones where it has been shown to form a zinc finger and to have protein-disulfide isomerase activity. Accordingly, PSA2 exhibited protein-disulfide reductase activity in vitro. PSA2 localized to the thylakoid lumen and was found in a ∼250-kDa complex harboring the peripheral PSI protein PsaG but lacking several core PSI subunits. PSA2 mRNA is coexpressed with mRNAs encoding various proteins involved in the biogenesis of the photosynthetic apparatus with peak expression preceding that of genes encoding structural components. PSA2 protein abundance was not decreased in the absence of PSI but was reduced in the absence of the PSI assembly factor Ycf3. These findings suggest that a complex harboring PSA2 and PsaG mediates thiol transactions in the thylakoid lumen that are important for the assembly of PSI.

A knockdown mutation of YELLOW-GREEN LEAF2 blocks chlorophyll biosynthesis in rice

An insert mutation of YELLOW-GREEN LEAF2 , encoding Heme Oxygenase 1 , results in significant reduction of its transcript levels, and therefore impairs chlorophyll biosynthesis in rice. Heme oxygenase (HO) in higher plants catalyzes the degradation of heme to synthesize phytochrome precursor and its roles conferring the photoperiodic control of flowering in rice have been revealed. However, its involvement in regulating rice chlorophyll (Chl) synthesis is not fully explored. In this study, we isolated a rice mutant named yellow-green leaf 2 (ygl2) from a (60)Co-irradiated population. Normal grown ygl2 seedlings showed yellow-green leaves with reduced contents of Chl and tetrapyrrole intermediates whereas an increase of Chl a/b ratio. Ultrastructural analyses demonstrated grana were poorly stacked in ygl2 mutant, resulting in underdevelopment of chloroplasts. The ygl2 locus was mapped to chromosome 6 and isolated via map-based cloning. Sequence analysis indicated that it encodes the rice HO1 and its identity was verified by transgenic complementation test and RNA interference. A 7-Kb insertion was found in the first exon of YGL2/HO1, resulting in significant reduction of YGL2 expressions in the ygl2 mutant. YGL2 was constitutively expressed in a variety of rice tissues with the highest levels in leaves and regulated by temperature. In addition, we found expression levels of some genes associated with Chl biosynthesis and photosynthesis were concurrently altered in ygl2 mutant. These results provide direct evidence that YGL2 has a vital function in rice Chl biosynthesis.

Mutation of the light-induced yellow leaf 1 gene, which encodes a geranylgeranyl reductase, affects chlorophyll biosynthesis and light sensitivity in rice

Chlorophylls (Chls) are crucial for capturing light energy for photosynthesis. Although several genes responsible for Chl biosynthesis were characterized in rice (Oryza sativa), the genetic properties of the hydrogenating enzyme involved in the final step of Chl synthesis remain unknown. In this study, we characterized a rice light-induced yellow leaf 1-1 (lyl1-1) mutant that is hypersensitive to high-light and defective in the Chl synthesis. Light-shading experiment suggested that the yellowing of lyl1-1 is light-induced. Map-based cloning of LYL1 revealed that it encodes a geranylgeranyl reductase. The mutation of LYL1 led to the majority of Chl molecules are conjugated with an unsaturated geranylgeraniol side chain. LYL1 is the firstly defined gene involved in the reduction step from Chl-geranylgeranylated (Chl(GG)) and geranylgeranyl pyrophosphate (GGPP) to Chl-phytol (Chl(Phy)) and phytyl pyrophosphate (PPP) in rice. LYL1 can be induced by light and suppressed by darkness which is consistent with its potential biological functions. Additionally, the lyl1-1 mutant suffered from severe photooxidative damage and displayed a drastic reduction in the levels of α-tocopherol and photosynthetic proteins. We concluded that LYL1 also plays an important role in response to high-light in rice.

The reduced plastid-encoded polymerase-dependent plastid gene expression leads to the delayed greening of the Arabidopsis fln2 mutant

In Arabidopsis leaf coloration mutants, the delayed greening phenomenon is common. Nonetheless, the mechanism remains largely elusive. Here, a delayed greening mutant fln2–4 of FLN2 (Fructokinase-Like Protein2) was studied. FLN2 is one component of Transcriptionally Active Chromosome (TAC) complex which is thought to contain the complete plastid-encoded polymerase (PEP). fln2–4 displayed albino phenotype on medium without sucrose. The PEP-dependent plastid gene expression and chloroplast development were inhibited in fln2–4. Besides interacting with thioredoxin z (TRX z), we identified that FLN2 interacted with another two members of TAC complex in yeast including its homologous protein FLN1 (Fructokinase-Like Protein1) and pTAC5. This indicates that FLN2 functions in regulation of PEP activity associated with these TAC components. fln2–4 exhibited delayed greening on sucrose-containing medium. Comparison of the PEP-dependent gene expression among two complete albino mutants (trx z and ptac14), two yellow mutants (ecb2–2 and ys1) and the fln2–4 showed that fln2–4 remains partial PEP activity. FLN2 and FLN1 are the target proteins of TRX z involved in affecting the PEP activity. Together with the data that FLN1 could interact with itself in yeast, FLN1 may form a homodimer to replace FLN1–FLN2 as the TRX z target in redox pathway for maintaining partial PEP activity in fln2–4. We proposed the partial PEP activity in the fln2 mutant allowed plastids to develop into fully functional chloroplasts when exogenous sucrose was supplied, and finally the mutants exhibited green phenotype.

Mutation of OsDET1 increases chlorophyll content in rice

As an important agronomic trait, the chlorophyll (Chl) content is closely related to photosynthesis in plants. A rice mutant Gc (Oryza sativa indica) was characterized previously by its enhanced Chl content (Chl b and total Chl) and exaggerated photosynthetic rate. Here, we describe the enhanced Chl content was caused by a mutation in the rice homolog of the DE-ETIOLATED1 (DET1) known to be involved in light transduction and morphogenesis in Arabidopsis and tomato. Sequence analysis revealed that the Gc mutant carried two fragment-insertions and a fragment-deletion upstream of the start codon of OsDET1, which led to enhance mRNA levels of OsDET1. Besides, the Gc mutant harbored a single T-to-C base transversion in the seventh exon of OsDET1, which resulted in leucine(328) to serine(328) localized in the highly conserved region. Genetic complementation demonstrated that OsDET1 mutation conferred the enhanced Chl content in the Gc mutant leaf. OsDET1 was richly expressed in green tissues, and its expression seems to be under circadian control. OsDET1-GFP fusion protein in onion epidermal cells showed that OsDET1 localized to the nucleus. These results indicated that OsDET1 mutation in Gc mutant increases Chl content in rice, which might be fundamental for enhanced photoresponsiveness.

Carotenoids, versatile components of oxygenic photosynthesis

Carotenoids (CARs) are a group of pigments that perform several important physiological functions in all kingdoms of living organisms. CARs serve as protective agents, which are essential structural components of photosynthetic complexes and membranes, and they play an important role in the light harvesting mechanism of photosynthesizing plants and cyanobacteria. The protection against reactive oxygen species, realized by quenching of singlet oxygen and the excited states of photosensitizing molecules, as well as by the scavenging of free radicals, is one of the main biological functions of CARs. X-ray crystallographic localization of CARs revealed that they are present at functionally and structurally important sites of both the PSI and PSII reaction centers. Characterization of a CAR-less cyanobacterial mutant revealed that while the absence of CARs prevents the formation of PSII complexes, it does not abolish the assembly and function of PSI. CAR molecules assist in the formation of protein subunits of the photosynthetic complexes by gluing together their protein components. In addition to their aforementioned indispensable functions, CARs have a substantial role in the formation and maintenance of proper cellular architecture, and potentially also in the protection of the translational machinery under stress conditions.

Photocurrent generation from surface assembled photosystem I on alkanethiol modified electrodes

Photosystem I (PSI) is a key component of oxygenic photosynthetic electron transport because of its light-induced electron transfer to the soluble electron acceptor ferredoxin. This work demonstrates the incorporation of surface assembled cyanobacterial trimeric PSI complexes into a biohybrid system for light-driven current generation. Specifically, this work demonstrates the improved assembly of PSI via electrophoretic deposition, with controllable surface assembled PSI density, on different self-assembled alkanethiol monolayers. Using artificial electron donors and acceptors (Os(bpy)(2)Cl(2) and methyl viologen) we demonstrate photocurrent generation from a single PSI layer, which remains photoactive for at least three hours of intermittent illumination. Photoelectrochemical comparison of the biohybrid systems assembled from different alkanethiols (hexanethiol, aminohexanethiol, mercaptohexanol, and mercaptohexanoic acid) reveals that the PSI generated photocurrent is enhanced by almost 5 times on negatively charged SAM surfaces as compared to positively charged surfaces. These results are discussed in light of how PSI is oriented upon electrodeposition on a SAM.

Young Leaf Chlorosis 1, a chloroplast-localized gene required for chlorophyll and lutein accumulation during early leaf development in rice

Chlorophyll (Chl) and lutein are the two most abundant and essential components in photosynthetic apparatus, and play critical roles in plant development. In this study, we characterized a rice mutant named young leaf chlorosis 1 (ylc1) from a ⁶⁰Co-irradiated population. Young leaves of the ylc1 mutant showed decreased levels of Chl and lutein compared to those of wild type, and transmission electron microscopy analysis revealed that the thylakoid lamellar structures were obviously loosely arranged. Whereas, the mutant turns green gradually and approaches normal green at the maximum tillering stage. The Young Leaf Chlorosis 1 (YLC1) gene was isolated via map-based cloning and identified to encode a protein of unknown function belonging to the DUF3353 superfamily. Complementation and RNA-interference tests confirmed the role of the YLC1 gene, which expressed in all tested rice tissues, especially in the leaves. Real-time PCR analyses showed that the expression levels of the genes associated with Chl biosynthesis and photosynthesis were affected in ylc1 mutant at different temperatures. In rice protoplasts, the YLC1 protein displayed a typical chloroplast location pattern. The N-terminal 50 amino acid residues were confirmed to be necessary and sufficient for chloroplast targeting. These data suggested that the YLC1 protein may be involved in Chl and lutein accumulation and chloroplast development at early leaf development in rice.

One divinyl reductase reduces the 8-vinyl groups in various intermediates of chlorophyll biosynthesis in a given higher plant species, but the isozyme differs between species

Divinyl reductase (DVR) converts 8-vinyl groups on various chlorophyll intermediates to ethyl groups, which is indispensable for chlorophyll biosynthesis. To date, five DVR activities have been detected, but adequate evidence of enzymatic assays using purified or recombinant DVR proteins has not been demonstrated, and it is unclear whether one or multiple enzymes catalyze these activities. In this study, we systematically carried out enzymatic assays using four recombinant DVR proteins and five divinyl substrates and then investigated the in vivo accumulation of various chlorophyll intermediates in rice (Oryza sativa), maize (Zea mays), and cucumber (Cucumis sativus). The results demonstrated that both rice and maize DVR proteins can convert all of the five divinyl substrates to corresponding monovinyl compounds, while both cucumber and Arabidopsis (Arabidopsis thaliana) DVR proteins can convert three of them. Meanwhile, the OsDVR (Os03g22780)-inactivated 824ys mutant of rice exclusively accumulated divinyl chlorophylls in its various organs during different developmental stages. Collectively, we conclude that a single DVR with broad substrate specificity is responsible for reducing the 8-vinyl groups of various chlorophyll intermediates in higher plants, but DVR proteins from different species have diverse and differing substrate preferences, although they are homologous.

Mapping QTL, epistasis and genotype × environment interaction of antioxidant activity, chlorophyll content and head formation in domesticated lettuce (Lactuca sativa)

Fruits and vegetables are rich sources of antioxidants in human diets and their intake is associated with chronic disease prevention. Lettuce (Lactuca sativa L.) is a common vegetable in diets worldwide, but its nutritional content is relatively low. To elucidate the genetic basis of antioxidant content in lettuce, we measured the oxygen radical absorbance capacity (ORAC) and chlorophyll (Chl) content as a proxy of β-carotene in an F(8) recombinant inbred line (RIL) in multiple production cycles at two different production sites. Plants were phenotyped at the open-leaf stage to measure genetic potential (GP) or at market maturity (MM) to measure the influence of head architecture ('head' or 'open'). Main effect quantitative trait loci (QTL) were identified at MM (three Chl and one ORAC QTL) and GP (two ORAC QTL). No main effect QTL for Chl was detected at GP, but epistatic interaction was identified in one pair of marker intervals for each trait at GP. Interactions with environment were also detected for both main and epistatic effects (two for main effect, and one for epistatic effect). Main effect QTL for plant architecture and nutritional traits at MM colocated to a single genomic region. Chlorophyll contents and ORAC values at MM were significantly higher and Chl a to Chl b ratios were lower in 'open' types compared to 'head' types. The nutritional traits assessed for GP showed a significant association with plant architecture suggesting pleiotropic effects or closely linked genes. Taken together, the antioxidant and chlorophyll content of lettuce is controlled by complex mechanisms and participating alleles change depending on growth stage and production environment.

Cytochrome c6-like protein as a putative donor of electrons to photosystem I in the cyanobacterium Nostoc sp. PCC 7119

Most organisms performing oxygenic photosynthesis contain either cytochrome c(6) or plastocyanin, or both, to transfer electrons from cytochrome b(6)-f to photosystem I. Even though plastocyanin has superseded cytochrome c(6) along evolution, plants contain a modified cytochrome c(6), the so called cytochrome c(6A), whose function still remains unknown. In this article, we describe a second cytochrome c(6) (the so called cytochrome c(6)-like protein), which is found in some cyanobacteria but is phylogenetically more related to plant cytochrome c(6A) than to cyanobacterial cytochrome c(6). In this article, we conclude that the cytochrome c(6)-like protein is a putative electron donor to photosystem I, but does play a role different to that of cytochrome c(6) and plastocyanin as it cannot accept electrons from cytochrome f. The existence of this third electron donor to PSI could explain why some cyanobacteria are able to grow photoautotrophically in the absence of both cytochrome c(6) and plastocyanin. In any way, the Cyt c(6)-like protein from Nostoc sp. PCC 7119 would be potentially utilized for the biohydrogen production, using cell-free photosystem I catalytic nanoparticles.

Identification of the 7-hydroxymethyl chlorophyll a reductase of the chlorophyll cycle in Arabidopsis

The interconversion of chlorophyll a and chlorophyll b, referred to as the chlorophyll cycle, plays a crucial role in the processes of greening, acclimation to light intensity, and senescence. The chlorophyll cycle consists of three reactions: the conversions of chlorophyll a to chlorophyll b by chlorophyllide a oxygenase, chlorophyll b to 7-hydroxymethyl chlorophyll a by chlorophyll b reductase, and 7-hydroxymethyl chlorophyll a to chlorophyll a by 7-hydroxymethyl chlorophyll a reductase. We identified 7-hydroxymethyl chlorophyll a reductase, which is the last remaining unidentified enzyme of the chlorophyll cycle, from Arabidopsis thaliana by genetic and biochemical methods. Recombinant 7-hydroxymethyl chlorophyll a reductase converted 7-hydroxymethyl chlorophyll a to chlorophyll a using ferredoxin. Both sequence and biochemical analyses showed that 7-hydroxymethyl chlorophyll a reductase contains flavin adenine dinucleotide and an iron-sulfur center. In addition, a phylogenetic analysis elucidated the evolution of 7-hydroxymethyl chlorophyll a reductase from divinyl chlorophyllide vinyl reductase. A mutant lacking 7-hydroxymethyl chlorophyll a reductase was found to accumulate 7-hydroxymethyl chlorophyll a and pheophorbide a. Furthermore, this accumulation of pheophorbide a in the mutant was rescued by the inactivation of the chlorophyll b reductase gene. The downregulation of pheophorbide a oxygenase activity is discussed in relation to 7-hydroxymethyl chlorophyll a accumulation.