Efficient operation of NAD(P)H dehydrogenase requires supercomplex formation with photosystem I via minor LHCI in Arabidopsis

Critical role of cyclic electron transport around photosystem I in the maintenance of photosystem I activity

In angiosperms, cyclic electron transport around photosystem I (PSI) is mediated by two pathways that depend on the PROTON GRADIENT REGULATION 5 (PGR5) protein and the chloroplast NADH dehydrogenase-like (NDH) complex, respectively. In the Arabidopsis double mutants defective in both pathways, plant growth and photosynthesis are impaired. The pgr5-1 mutant used in the original study is a missense allele and accumulates low levels of PGR5 protein. In this study, we generated two knockout (KO) alleles, designated as pgr5-5 and pgr5-6, using the CRISPR-Cas9 technology. Although both KO alleles showed a severe reduction in P700 similar to the pgr5-1 allele, NPQ induction was less severely impaired in the KO alleles than in the pgr5-1 allele. In the pgr5-1 allele, the second mutation affecting NPQ size was mapped to ~21 cM south of the pgr5-1 locus. Overexpression of the pgr5-1 allele, encoding the glycine130-to-serine change, complemented the pgr5-5 phenotype, suggesting that the pgr5-1 mutation destabilizes PGR5 but that the mutant protein retains partial functionality. Using two KO alleles, we created the double mutants with two chlororespiratory reduction (crr) mutants defective in the NDH complex. The growth of the double mutants was notably impaired. In the double mutant seedlings that survived on the medium containing sucrose, PSI activity evaluated by the P700 oxidation was severely impaired, whereas PSII activity was only mildly impaired. Cyclic electron transport around PSI is required to maintain PSI activity.

Immunophilin FKB20-2 participates in oligomerization of Photosystem I in Chlamydomonas

PSI is a sophisticated photosynthesis protein complex that fuels the light reaction of photosynthesis in algae and vascular plants. While the structure and function of PSI have been studied extensively, the dynamic regulation on PSI oligomerization and high light response is less understood. In this work, we characterized a high light-responsive immunophilin gene FKB20-2 (FK506-binding protein 20-2) required for PSI oligomerization and high light tolerance in Chlamydomonas (Chlamydomonas reinhardtii). Biochemical assays and 77-K fluorescence measurement showed that loss of FKB20-2 led to the reduced accumulation of PSI core subunits and abnormal oligomerization of PSI complexes and, particularly, reduced PSI intermediate complexes in fkb20-2. It is noteworthy that the abnormal PSI oligomerization was observed in fkb20-2 even under dark and dim light growth conditions. Coimmunoprecipitation, MS, and yeast 2-hybrid assay revealed that FKB20-2 directly interacted with the low molecular weight PSI subunit PsaG, which might be involved in the dynamic regulation of PSI-light-harvesting complex I supercomplexes. Moreover, abnormal PSI oligomerization caused accelerated photodamage to PSII in fkb20-2 under high light stress. Together, we demonstrated that immunophilin FKB20-2 affects PSI oligomerization probably by interacting with PsaG and plays pivotal roles during Chlamydomonas tolerance to high light.

Transcriptome analysis of the effects of different carbon dioxide concentrations on paramylon accumulation in Euglena gracilis Z

Appropriate concentration of carbon dioxide (CO2) will promote algae growth and metabolism. Building upon this finding, the present study investigated the impact of different CO2 concentrations (5% and 20%) on the carbon sequestration capacity of E. gracilis through aeration culturing, employing a combination of physiological analyses and transcriptome analysis. The results demonstrated that under 5% CO2 concentration, the cell density of E. gracilis was 1.79 times higher than that achieved in an air culture condition, and the paramylon content of E. gracilis was found to be 6.18 times higher than that of the air group. Based on transcriptome analysis, the carbon metabolism of E. gracilis was discussed. Significant up-regulation expression of genes associated with carbon synthesis was validated by an increase in paramylon content. This study revealed that under 5% CO2 conditions, E. gracilis exhibited elevated growth rate and enhanced photosynthetic carbon assimilation efficiency.

NdhS interacts with cytochrome b6 f to form a complex in Arabidopsis

Cyclic electron transport (CET) around photosystem I (PSI) is crucial for photosynthesis to perform photoprotection and sustain the balance of ATP and NADPH. However, the critical component of CET, cyt b6 f complex (cyt b6 f), functions in CET has yet to be understood entirely. In this study, we found that NdhS, a subunit of NADPH dehydrogenase-like (NDH) complex, interacted with cyt b6 f to form a complex in Arabidopsis. This interaction depended on the N-terminal extension of NdhS, which was conserved in eukaryotic plants but defective in prokaryotic algae. The migration of NdhS was much more in cyt b6 f than in PSI-NDH super-complex. Based on these results, we suggested that NdhS and NADP+ oxidoreductase provide a docking domain for the mobile electron carrier ferredoxin to transfer electrons to the plastoquinone pool via cyt b6 f in eukaryotic photosynthesis.

Identification of Two Flip-Over Genes in Grass Family as Potential Signature of C4 Photosynthesis Evolution

In flowering plants, C4 photosynthesis is superior to C3 type in carbon fixation efficiency and adaptation to extreme environmental conditions, but the mechanisms behind the assembly of C4 machinery remain elusive. This study attempts to dissect the evolutionary divergence from C3 to C4 photosynthesis in five photosynthetic model plants from the grass family, using a combined comparative transcriptomics and deep learning technology. By examining and comparing gene expression levels in bundle sheath and mesophyll cells of five model plants, we identified 16 differentially expressed signature genes showing cell-specific expression patterns in C3 and C4 plants. Among them, two showed distinctively opposite cell-specific expression patterns in C3 vs. C4 plants (named as FOGs). The in silico physicochemical analysis of the two FOGs illustrated that C3 homologous proteins of LHCA6 had low and stable pI values of ~6, while the pI values of LHCA6 homologs increased drastically in C4 plants Setaria viridis (7), Zea mays (8), and Sorghum bicolor (over 9), suggesting this protein may have different functions in C3 and C4 plants. Interestingly, based on pairwise protein sequence/structure similarities between each homologous FOG protein, one FOG PGRL1A showed local inconsistency between sequence similarity and structure similarity. To find more examples of the evolutionary characteristics of FOG proteins, we investigated the protein sequence/structure similarities of other FOGs (transcription factors) and found that FOG proteins have diversified incompatibility between sequence and structure similarities during grass family evolution. This raised an interesting question as to whether the sequence similarity is related to structure similarity during C4 photosynthesis evolution.

The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas

Tomato (Solanum lycopersicum) is a model species for studying fruit development, wounding, herbivory, and pathogen attack. Despite tomato's world-wide economic importance and the role of chloroplasts as metabolic hubs and integrators of environmental cues, little is known about the stromal proteome of tomato. Using a high-yielding protocol for chloroplast and stromal protein isolation, MudPIT nano-LC-MS/MS analyses, a robust in-house protein database (the Atlas) for predicting the plastid localization of tomato proteins, and rigorous selection criteria for inclusion/exclusion in the stromal proteome, we identified 1,278 proteins of the tomato stromal proteome. We provide one of the most robust stromal proteomes available to date with empirical evidence for 545 and 92 proteins not previously described for tomato plastids and the Arabidopsis stroma, respectively. The relative abundance of tomato stromal proteins was determined using the exponentially modified protein abundance index (emPAI). Comparison of the abundance of tomato and Arabidopsis stromal proteomes provided evidence for the species-specific nature of stromal protein homeostasis. The manual curation of the tomato stromal proteome classified proteins into ten functional categories resulting in an accessible compendium of tomato chloroplast proteins. After curation, only 91 proteins remained as unknown, uncharacterized or as enzymes with unknown functions. The curation of the tomato stromal proteins also indicated that tomato has a number of paralogous proteins, not present in Arabidopsis, which accumulated to different levels in chloroplasts. As some of these proteins function in key metabolic pathways or in perceiving or transmitting signals critical for plant adaptation to biotic and abiotic stress, these data suggest that tomato may modulate the bidirectional communication between chloroplasts and nuclei in a novel manner. The stromal proteome provides a fertile ground for future mechanistic studies in the field of tomato chloroplast-nuclear signaling and are foundational for our goal of elucidating the dynamics of the stromal proteome controlled by the solanaceous-specific, stromal, and wound-inducible leucine aminopeptidase A of tomato.

Flavodiiron-mediated O2 photoreduction at photosystem I acceptor-side provides photoprotection to conifer thylakoids in early spring

Green organisms evolve oxygen (O₂) via photosynthesis and consume it by respiration. Generally, net O₂ consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O₂ consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O₂ consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O₂ photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.

STN7 is not essential for developmental acclimation of Arabidopsis to light intensity

Plants respond to changing light intensity in the short term through regulation of light harvesting, electron transfer, and metabolism to mitigate redox stress. A sustained shift in light intensity leads to a long-term acclimation response (LTR). This involves adjustment in the stoichiometry of photosynthetic complexes through de novo synthesis and degradation of specific proteins associated with the thylakoid membrane. The light-harvesting complex II (LHCII) serine/threonine kinase STN7 plays a key role in short-term light harvesting regulation and was also suggested to be crucial to the LTR. Arabidopsis plants lacking STN7 (stn7) shifted to low light experience higher photosystem II (PSII) redox pressure than the wild type or those lacking the cognate phosphatase TAP38 (tap38), while the reverse is true at high light, where tap38 suffers more. In principle, the LTR should allow optimisation of the stoichiometry of photosynthetic complexes to mitigate these effects. We used quantitative label-free proteomics to assess how the relative abundance of photosynthetic proteins varied with growth light intensity in wild-type, stn7, and tap38 plants. All plants were able to adjust photosystem I, LHCII, cytochrome b6 f, and ATP synthase abundance with changing white light intensity, demonstrating neither STN7 nor TAP38 is crucial to the LTR per se. However, stn7 plants grown for several weeks at low light (LL) or moderate light (ML) still showed high PSII redox pressure and correspondingly lower PSII efficiency, CO2 assimilation, and leaf area compared to wild-type and tap38 plants, hence the LTR is unable to fully ameliorate these symptoms. In contrast, under high light growth conditions the mutants and wild type behaved similarly. These data are consistent with the paramount role of STN7-dependent LHCII phosphorylation in tuning PSII redox state for optimal growth in LL and ML conditions.

Dynamic Regulation of the Light-Harvesting System through State Transitions in Land Plants and Green Algae

Photosynthesis constitutes the only known natural process that captures the solar energy to convert carbon dioxide and water into biomass. The primary reactions of photosynthesis are catalyzed by the photosystem II (PSII) and photosystem I (PSI) complexes. Both photosystems associate with antennae complexes whose main function is to increase the light-harvesting capability of the core. In order to maintain optimal photosynthetic activity under a constantly changing natural light environment, plants and green algae regulate the absorbed photo-excitation energy between PSI and PSII through processes known as state transitions. State transitions represent a short-term light adaptation mechanism for balancing the energy distribution between the two photosystems by relocating light-harvesting complex II (LHCII) proteins. The preferential excitation of PSII (state 2) results in the activation of a chloroplast kinase which in turn phosphorylates LHCII, a process followed by the release of phosphorylated LHCII from PSII and its migration to PSI, thus forming the PSI-LHCI-LHCII supercomplex. The process is reversible, as LHCII is dephosphorylated and returns to PSII under the preferential excitation of PSI. In recent years, high-resolution structures of the PSI-LHCI-LHCII supercomplex from plants and green algae were reported. These structural data provide detailed information on the interacting patterns of phosphorylated LHCII with PSI and on the pigment arrangement in the supercomplex, which is critical for constructing the excitation energy transfer pathways and for a deeper understanding of the molecular mechanism of state transitions progress. In this review, we focus on the structural data of the state 2 supercomplex from plants and green algae and discuss the current state of knowledge concerning the interactions between antenna and the PSI core and the potential energy transfer pathways in these supercomplexes.

Genetic control of tolerance to drought stress in soybean

BACKGROUND

Drought stress limits the production of soybean [Glycine max (L.) Merr.], which is the most grown high-value legume crop worldwide. Breeding for drought tolerance is a difficult endeavor and understanding the genetic basis of drought tolerance in soybean is therefore crucial for harnessing the genomic regions involved in the tolerance mechanisms. A genome-wide association study (GWAS) analysis was applied in a soybean germplasm collection (the EUCLEG collection) of 359 accessions relevant for breeding in Europe, to identify genomic regions and candidate genes involved in the response to short duration and long duration drought stress (SDS and LDS respectively) in soybean.

RESULTS

The phenotypic response to drought was stronger in the long duration drought (LDS) than in the short duration drought (SDS) experiment. Over the four traits considered (canopy wilting, leaf senescence, maximum absolute growth rate and maximum plant height) the variation was in the range of 8.4-25.2% in the SDS, and 14.7-29.7% in the LDS experiments. The GWAS analysis identified a total of 17 and 22 significant marker-trait associations for four traits in the SDS and LDS experiments, respectively. In the genomic regions delimited by these markers we identified a total of 12 and 16 genes with putative functions that are of particular relevance for drought stress responses including stomatal movement, root formation, photosynthesis, ABA signaling, cellular protection and cellular repair mechanisms. Some of these genomic regions co-localized with previously known QTLs for drought tolerance traits including water use efficiency, chlorophyll content and photosynthesis.

CONCLUSION

Our results indicate that the mechanism of slow wilting in the SDS might be associated with the characteristics of the root system, whereas in the LDS, slow wilting could be due to low stomatal conductance and transpiration rates enabling a high WUE. Drought-induced leaf senescence was found to be associated to ABA and ROS responses. The QTLs related to WUE contributed to growth rate and canopy height maintenance under drought stress. Co-localization of several previously known QTLs for multiple agronomic traits with the SNPs identified in this study, highlights the importance of the identified genomic regions for the improvement of agronomic performance in addition to drought tolerance in the EUCLEG collection.

The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency

Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C₃ plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light-use efficiency at high irradiance as identified in a small number of exceptional C₃ species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light-use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light-saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light-use efficiency and enhancing photosynthetic rates in crop species.

Quantitative proteomics reveals redox-based functional regulation of photosynthesis under fluctuating light in plants

Photosynthesis involves a series of redox reactions and is the major source of reactive oxygen species in plant cells. Fluctuating light (FL) levels, which occur commonly in natural environments, affect photosynthesis; however, little is known about the specific effects of FL on the redox regulation of photosynthesis. Here, we performed global quantitative mapping of the Arabidopsis thaliana cysteine thiol redox proteome under constant light and FL conditions. We identified 8857 redox-switched thiols in 4350 proteins, and 1501 proteins that are differentially modified depending on light conditions. Notably, proteins related to photosynthesis, especially photosystem I (PSI), are operational thiol-switching hotspots. Exposure of wild-type A. thaliana to FL resulted in decreased PSI abundance, stability, and activity. Interestingly, in response to PSI photodamage, more of the PSI assembly factor PSA3 dynamically switches to the reduced state. Furthermore, the Cys199 and Cys200 sites in PSA3 are necessary for its full function. Moreover, thioredoxin m (Trx m) proteins play roles in redox switching of PSA3, and are required for PSI activity and photosynthesis. This study thus reveals a mechanism for redox-based regulation of PSI under FL, and provides insight into the dynamic acclimation of photosynthesis in a changing environment.

Native architecture and acclimation of photosynthetic membranes in a fast-growing cyanobacterium

Efficient solar energy conversion is ensured by the organization, physical association, and physiological coordination of various protein complexes in photosynthetic membranes. Here, we visualize the native architecture and interactions of photosynthetic complexes within the thylakoid membranes from a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) using high-resolution atomic force microscopy. In the Syn2973 thylakoid membranes, both photosystem I (PSI)-enriched domains and crystalline photosystem II (PSII) dimer arrays were observed, providing favorable membrane environments for photosynthetic electron transport. The high light (HL)-adapted thylakoid membranes accommodated a large amount of PSI complexes, without the incorporation of iron-stress-induced protein A (IsiA) assemblies and formation of IsiA-PSI supercomplexes. In the iron deficiency (Fe-)-treated thylakoid membranes, in contrast, IsiA proteins densely associated with PSI, forming the IsiA-PSI supercomplexes with varying assembly structures. Moreover, type-I NADH dehydrogenase-like complexes (NDH-1) were upregulated under the HL and Fe- conditions and established close association with PSI complexes to facilitate cyclic electron transport. Our study provides insight into the structural heterogeneity and plasticity of the photosynthetic apparatus in the context of their native membranes in Syn2973 under environmental stress. Advanced understanding of the photosynthetic membrane organization and adaptation will provide a framework for uncovering the molecular mechanisms of efficient light harvesting and energy conversion.

Ascorbate peroxidase postcold regulation of chloroplast NADPH dehydrogenase activity controls cold memory

Exposure of Arabidopsis (Arabidopsis thaliana) to 4°C imprints a cold memory that modulates gene expression in response to a second (triggering) stress stimulus applied several days later. Comparison of plastid transcriptomes of cold-primed and control plants directly before they were exposed to the triggering stimulus showed downregulation of several subunits of chloroplast NADPH dehydrogenase (NDH) and regulatory subunits of ATP synthase. NDH is, like proton gradient 5 (PGR5)-PGR5-like1 (PGRL1), a thylakoid-embedded, ferredoxin-dependent plastoquinone reductase that protects photosystem I and stabilizes ATP synthesis by cyclic electron transport (CET). Like PGRL1A and PGRL1B transcript levels, ndhA and ndhD transcript levels decreased during the 24-h long priming cold treatment. PGRL1 transcript levels were quickly reset in the postcold phase, but expression of ndhA remained low. The transcript abundances of other ndh genes decreased within the next days. Comparison of thylakoid-bound ascorbate peroxidase (tAPX)-free and transiently tAPX-overexpressing or tAPX-downregulating Arabidopsis lines demonstrated that ndh expression is suppressed by postcold induction of tAPX. Four days after cold priming, when tAPX protein accumulation was maximal, NDH activity was almost fully lost. Lack of the NdhH-folding chaperonin Crr27 (Cpn60β4), but not lack of the NDH activity modulating subunits NdhM, NdhO, or photosynthetic NDH subcomplex B2 (PnsB2), strengthened priming regulation of zinc finger of A. thaliana 10, which is a nuclear-localized target gene of the tAPX-dependent cold-priming pathway. We conclude that cold-priming modifies chloroplast-to-nucleus stress signaling by tAPX-mediated suppression of NDH-dependent CET and that plastid-encoded NdhH, which controls subcomplex A assembly, is of special importance for memory stabilization.

Structural elucidation of vascular plant photosystem I and its functional implications

In vascular plants, bryophytes and algae, the photosynthetic light reaction takes place in the thylakoid membrane where two transmembrane supercomplexes PSII and PSI work together with cytochrome b 6 f and ATP synthase to harvest the light energy and produce ATP and NADPH. Vascular plant PSI is a 600-kDa protein-pigment supercomplex, the core complex of which is partly surrounded by peripheral light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core to be used for charge separation. PSI is unique mainly in absorption of longer-wavelengths than PSII, fast excitation energy transfer including uphill energy transfer, and an extremely high quantum efficiency. From the early 1980s, a lot of effort has been dedicated to structural and functional studies of PSI-LHCI, leading to the current understanding of how more than 200 cofactors are kept at the correct distance and geometry to facilitate fast energy transfer in this supercomplex at an atomic level. In this review, we review the history of studies on vascular plant PSI-LHCI, summarise the present research progress on its structure, and present some new and further questions to be answered in future studies.

Assembly of LHCA5 into PSI blue shifts the far-red fluorescence emission in higher plants

In higher plants, the PSI core complex is associated with light-harvesting complex I (LHCI), forming the PSI-LHCI super-complex. In vascular plants, four major antenna proteins (LHCA1-4) are assembled in the order of LHCA1, LHCA4, LHCA2, and LHCA3 into a crescent-shaped LHCI, while LHCA5 and LHCA6 are minor antenna proteins. By contrast, in moss and green algae, LHCA5 or LHCA5-like protein functions as one of the major antenna proteins by residing at the second site of LHCI. In order to learn the effect of binding different LHCA proteins, i.e. LHCA4 or LHCA5, within the PSI-LHCI super-complex on photosynthetic properties of plants, we constructed LHCA5 overexpression plants with a wild type (WT) background and an lhca4 mutant background in Arabidopsis thaliana. The results showed that: (i) there are little difference in phenotype, pigment composition and chlorophyll fluorescence parameters between the transgenic Arabidopsis and their corresponding background materials; (ii) in spite of a small amount of LHCA5, the LHCA5-included PSI-LHCI super-complex can be obtained by extracting samples incubated with anti-FLAG M2 Affinity Gel, in which LHCA5 is found to substitute for LHCA4 as analyzed by immunoblotting analysis; (iii) the replacement of LHCA4 with LHCA5 within PSI-LHCI super-complex leads to a blue shift in low temperature fluorescence emission, suggesting a decrease in far-red absorbance. These results provide new clues for understanding the position and function of LHCA4 and LHCA5 during the evolution of green plants from aquatic to terrestrial lifestyles.

Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana

Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane-embedded NADH dehydrogenase-like (NDH) complex that contains at least 29 protein subunits and associates with photosystem I (PSI) to form the NDH-PSI supercomplex. Here, we report the 3.9 Å resolution structure of the Arabidopsis thaliana NDH-PSI (AtNDH-PSI) supercomplex. We constructed structural models for 26 AtNDH subunits, among which 11 are unique to chloroplasts and stabilize the core part of the NDH complex. In the supercomplex, one NDH can bind up to two PSI-light-harvesting complex I (PSI-LHCI) complexes at both sides of its membrane arm. Two minor LHCIs, Lhca5 and Lhca6, each present in one PSI-LHCI, interact with NDH and contribute to supercomplex formation and stabilization. Collectively, our study reveals the structural details of the AtNDH-PSI supercomplex assembly and provides a molecular basis for further investigation of the regulatory mechanism of CEF in plants.

Qualitative and quantitative evaluation of thylakoid complexes separated by Blue Native PAGE

BACKGROUND

Blue Native polyacrylamide gel electrophoresis (BN PAGE) followed by denaturing PAGE is a widely used, convenient and time efficient method to separate thylakoid complexes and study their composition, abundance, and interactions. Previous analyses unravelled multiple monomeric and dimeric/oligomeric thylakoid complexes but, in certain cases, the separation of complexes was not proper. Particularly, the resolution of super- and megacomplexes, which provides important information on functional interactions, still remained challenging.

RESULTS

Using a detergent mixture of 1% (w/V) n-dodecyl-β-D-maltoside plus 1% (w/V) digitonin for solubilisation and 4.3-8% gel gradients for separation as methodological improvements in BN PAGE, several large photosystem (PS) I containing bands were detected. According to BN(/BN)/SDS PAGE and mass spectrometry analyses, these PSI bands proved to be PSI-NADH dehydrogenase-like megacomplexes more discernible in maize bundle sheath thylakoids, and PSI complexes with different light-harvesting complex (LHC) complements (PSI-LHCII, PSI-LHCII*) more abundant in mesophyll thylakoids of lincomycin treated maize. For quantitative determination of the complexes and their comparison across taxa and physiological conditions, sample volumes applicable to the gel, correct baseline determination of the densitograms, evaluation methods to resolve complexes running together, calculation of their absolute/relative amounts and distribution among their different forms are proposed.

CONCLUSIONS

Here we report our experience in Blue/Clear-Native polyacrylamide gel electrophoretic separation of thylakoid complexes, their identification, quantitative determination and comparison in different samples. The applied conditions represent a powerful methodology for the analysis of thylakoid mega- and supercomplexes.

OTP970 Is Required for RNA Editing of Chloroplast ndhB Transcripts in Arabidopsis thaliana

RNA editing is essential for compensating for defects or mutations in haploid organelle genomes and is regulated by numerous trans-factors. Pentatricopeptide repeat (PPR) proteins are the prime factors that are involved in RNA editing; however, many have not yet been identified. Here, we screened the plastid-targeted PLS-DYW subfamily of PPR proteins belonging to Arabidopsis thaliana and identified ORGANELLE TRANSCRIPT PROCESSING 970 (OTP970) as a key player in RNA editing in plastids. A loss-of-function otp970 mutant was impaired in RNA editing of ndhB transcripts at site 149 (ndhB-C149). RNA-immunoprecipitation analysis indicated that OTP970 was associated with the ndhB-C149 site. The complementation of the otp970 mutant with OTP970 lacking the DYW domain (OTP970^∆DYW) failed to restore the RNA editing of ndhB-C149. ndhB gene encodes the B subunit of the NADH dehydrogenase-like (NDH) complex; however, neither NDH activity and stability nor NDH-PSI supercomplex formation were affected in otp970 mutant compared to the wild type, indicating that alteration in amino acid sequence is not necessary for NdhB function. Together, these results suggest that OTP970 is involved in the RNA editing of ndhB-C149 and that the DYW domain is essential for its function.

Genome-Wide Investigation of the PtrCHLP Family Reveals That PtrCHLP3 Actively Mediates Poplar Growth and Development by Regulating Photosynthesis

Chlorophyll (Chl) plays a crucial role in plant photosynthesis. The geranylgeraniol reductase gene (CHLP) participates in the terminal hydrogenation of chlorophyll biosynthesis. Although there are many studies related to the genome-wide analysis of Populus trichocarpa, little research has been conducted on CHLP family genes, especially those concerning growth and photosynthesis. In this study, three CHLP genes were identified in Populus. The evolutionary tree indicated that the CHLP family genes were divided into six groups. Moreover, one pair of genes was derived from segmental duplications in Populus. Many elements related to growth were detected by cis-acting element analysis of the promoters of diverse PtrCHLPs. Furthermore, PtrCHLPs exhibit different tissue expression patterns. In addition, PtrCHLP3 is preferentially expressed in the leaves and plays an important role in regulating chlorophyll biosynthesis. Silencing of PtrCHLP3 in poplar resulted in a decrease in chlorophyll synthesis in plants, thus blocking electron transport during photosynthesis. Furthermore, inhibition of PtrCHLP3 expression in poplar can inhibit plant growth through the downregulation of photosynthesis. Ultimately, PtrCHLP3 formed a co-expression network with photosynthesis and chlorophyll biosynthesis-related genes, which synergistically affected the growth and photosynthesis of poplars. Thus, this study provides genetic resources for the improved breeding of fast-growing tree traits.

Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare

The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET)^1-3. The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET.

Critical Role of NdhA in the Incorporation of the Peripheral Arm into the Membrane-Embedded Part of the Chloroplast NADH Dehydrogenase-Like Complex

The chloroplast NADH dehydrogenase-like (NDH) complex mediates ferredoxin-dependent plastoquinone reduction in the thylakoid membrane. In angiosperms, chloroplast NDH is composed of five subcomplexes and further forms a supercomplex with photosystem I (PSI). Subcomplex A (SubA) mediates the electron transport and consists of eight subunits encoded by both plastid and nuclear genomes. The assembly of SubA in the stroma has been extensively studied, but it is unclear how SubA is incorporated into the membrane-embedded part of the NDH complex. Here, we isolated a novel Arabidopsis mutant chlororespiratory reduction 16 (crr16) defective in NDH activity. CRR16 encodes a chloroplast-localized P-class pentatricopeptide repeat protein conserved in angiosperms. Transcript analysis of plastid-encoded ndh genes indicated that CRR16 was responsible for the efficient splicing of the group II intron in the ndhA transcript, which encodes a membrane-embedded subunit localized to the connecting site between SubA and the membrane subcomplex (SubM). To analyze the roles of NdhA in the assembly and stability of the NDH complex, the homoplastomic knockout plant of ndhA (ΔndhA) was generated in tobacco (Nicotiana tabacum). Biochemical analyses of crr16 and ΔndhA plants indicated that NdhA was essential for stabilizing SubA and SubE but not for the accumulation of the other three subcomplexes. Furthermore, the crr16 mutant accumulated the SubA assembly intermediates in the stroma more than that in the wild type. These results suggest that NdhA biosynthesis is essential for the incorporation of SubA into the membrane-embedded part of the NDH complex at the final assembly step of the NDH-PSI supercomplex.

Comparative proteomics of thylakoids from Arabidopsis grown in laboratory and field conditions

Compared to controlled laboratory conditions, plant growth in the field is rarely optimal since it is frequently challenged by large fluctuations in light and temperature which lower the efficiency of photosynthesis and lead to photo-oxidative stress. Plants grown under natural conditions therefore place an increased onus on the regulatory mechanisms that protect and repair the delicate photosynthetic machinery. Yet, the exact changes in thylakoid proteome composition which allow plants to acclimate to the natural environment remain largely unexplored. Here, we use quantitative label-free proteomics to demonstrate that field-grown Arabidopsis plants incorporate aspects of both the low and high light acclimation strategies previously observed in laboratory-grown plants. Field plants showed increases in the relative abundance of ATP synthase, cytochrome b 6 f, ferredoxin-NADP+ reductases (FNR1 and FNR2) and their membrane tethers TIC62 and TROL, thylakoid architecture proteins CURT1A, CURT1B, RIQ1, and RIQ2, the minor monomeric antenna complex CP29.3, rapidly-relaxing non-photochemical quenching (qE)-related proteins PSBS and VDE, the photosystem II (PSII) repair machinery and the cyclic electron transfer complexes NDH, PGRL1B, and PGR5, in addition to decreases in the amounts of LHCII trimers composed of LHCB1.1, LHCB1.2, LHCB1.4, and LHCB2 proteins and CP29.2, all features typical of a laboratory high light acclimation response. Conversely, field plants also showed increases in the abundance of light harvesting proteins LHCB1.3 and CP29.1, zeaxanthin epoxidase (ZEP) and the slowly-relaxing non-photochemical quenching (qI)-related protein LCNP, changes previously associated with a laboratory low light acclimation response. Field plants also showed distinct changes to the proteome including the appearance of stress-related proteins ELIP1 and ELIP2 and changes to proteins that are largely invariant under laboratory conditions such as state transition related proteins STN7 and TAP38. We discuss the significance of these alterations in the thylakoid proteome considering the unique set of challenges faced by plants growing under natural conditions.

Thioredoxins m are major players in the multifaceted light-adaptive response in Arabidopsis thaliana

Thioredoxins (TRXs) are well-known redox signalling players, which carry out post-translational modifications in target proteins. Chloroplast TRXs are divided into different types and have central roles in light energy uptake and the regulation of primary metabolism. The isoforms TRX m1, m2, and m4 from Arabidopsis thaliana are considered functionally related. Knowing their key position in the hub of plant metabolism, we hypothesized that the impairment of the TRX m signalling would not only have harmful consequences on chloroplast metabolism but also at different levels of plant development. To uncover the physiological and developmental processes that depend on TRX m signalling, we carried out a comprehensive study of Arabidopsis single, double, and triple mutants defective in the TRX m1, m2, and m4 proteins. As light and redox signalling are closely linked, we investigated the response to high light (HL) of the plants that are gradually compromised in TRX m signalling. We provide experimental evidence relating the lack of TRX m and the appearance of novel phenotypic features concerning mesophyll structure, stomata biogenesis, and stomatal conductance. We also report new data indicating that the isoforms of TRX m fine-tune the response to HL, including the accumulation of the protective pigment anthocyanin. These results reveal novel signalling functions for the TRX m and underline their importance for plant growth and fulfilment of the acclimation/response to HL conditions.

Characterizing the supercomplex association of photosynthetic complexes in cyanobacteria

The light reactions of photosynthesis occur in thylakoid membranes that are densely packed with a series of photosynthetic complexes. The lateral organization and close association of photosynthetic complexes in native thylakoid membranes are vital for efficient light harvesting and energy transduction. Recently, analysis of the interconnections between photosynthetic complexes to form supercomplexes has garnered great interest. In this work, we report a method integrating immunoprecipitation, mass spectrometry and atomic force microscopy to identify the inter-complex associations of photosynthetic complexes in thylakoid membranes from the cyanobacterium Synechococcus elongatus PCC 7942. We characterize the preferable associations between individual photosynthetic complexes and binding proteins involved in the complex-complex interfaces, permitting us to propose the structural models of photosynthetic complex associations that promote the formation of photosynthetic supercomplexes. We also identified other potential binding proteins with the photosynthetic complexes, suggesting the highly connecting networks associated with thylakoid membranes. This study provides mechanistic insight into the physical interconnections of photosynthetic complexes and potential partners, which are crucial for efficient energy transfer and physiological acclimatization of the photosynthetic apparatus. Advanced knowledge of the protein organization and interplay of the photosynthetic machinery will inform rational design and engineering of artificial photosynthetic systems to supercharge energy production.

Whole genome duplication facilitated the evolution of C4 photosynthesis in Gynandropsis gynandra

In higher plants, whole-genome duplication (WGD) is thought to facilitate the evolution of C₄ photosynthesis from C₃ photosynthesis. To understand this issue, we used new and existing leaf-development transcriptomes to construct two coding sequence databases for C₄Gynandropsis gynandra and C₃Tarenaya hassleriana, which shared a WGD before their divergence. We compared duplicated genes in the two species and found that the WGD contributed to four aspects of the evolution of C₄ photosynthesis in G. gynandra. First, G. gynandra has retained the duplicates of ALAAT (alanine aminotransferase) and GOGAT (glutamine oxoglutarate aminotransferase) for nitrogen recycling to establish a photorespiratory CO₂ pump in bundle sheath (BS) cells for increasing photosynthesis efficiency, suggesting that G. gynandra experienced a C₃–C₄ intermediate stage during the C₄ evolution. Second, G. gynandra has retained almost all known vein-development-related paralogous genes derived from the WGD event, likely contributing to the high vein complexity of G. gynandra. Third, the WGD facilitated the evolution of C₄ enzyme genes and their recruitment into the C₄ pathway. Fourth, several genes encoding photosystem I proteins were derived from the WGD and are upregulated in G. gynandra, likely enabling the NADH dehydrogenase-like complex to produce extra ATPs for the C₄ CO₂ concentration mechanism. Thus, the WGD apparently played an enabler role in the evolution of C₄ photosynthesis in G. gynandra. Importantly, an ALAAT duplicate became highly expressed in BS cells in G. gynandra, facilitating nitrogen recycling and transition to the C₄ cycle. This study revealed how WDG may facilitate C₄ photosynthesis evolution.

Evolution of an assembly factor-based subunit contributed to a novel NDH-PSI supercomplex formation in chloroplasts

Chloroplast NADH dehydrogenase-like (NDH) complex is structurally related to mitochondrial Complex I and forms a supercomplex with two copies of Photosystem I (the NDH-PSI supercomplex) via linker proteins Lhca5 and Lhca6. The latter was acquired relatively recently in a common ancestor of angiosperms. Here we show that NDH-dependent Cyclic Electron Flow 5 (NDF5) is an NDH assembly factor in Arabidopsis. NDF5 initiates the assembly of NDH subunits (PnsB2 and PnsB3) and Lhca6, suggesting that they form a contact site with Lhca6. Our analysis of the NDF5 ortholog in Physcomitrella and angiosperm genomes reveals the subunit PnsB2 to be newly acquired via tandem gene duplication of NDF5 at some point in the evolution of angiosperms. Another Lhca6 contact subunit, PnsB3, has evolved from a protein unrelated to NDH. The structure of the largest photosynthetic electron transport chain complex has become more complicated by acquiring novel subunits and supercomplex formation with PSI.

The chloroplast NDH complex interacts with Photosystem I to form the NDH-PSI supercomplex. Here the authors show that Arabidopsis NDF5 shares a common ancestor with the NDH subunit PnsB2 and acts as an NDH assembly factor initiating the assembly of PnsB2 and the evolutionarily distinct PnsB3.

Light Harvesting in Fluctuating Environments: Evolution and Function of Antenna Proteins across Photosynthetic Lineage

Photosynthesis is the major natural process that can harvest and harness solar energy into chemical energy. Photosynthesis is performed by a vast number of organisms from single cellular bacteria to higher plants and to make the process efficient, all photosynthetic organisms possess a special type of pigment protein complex(es) that is (are) capable of trapping light energy, known as photosynthetic light-harvesting antennae. From an evolutionary point of view, simpler (unicellular) organisms typically have a simple antenna, whereas higher plants possess complex antenna systems. The higher complexity of the antenna systems provides efficient fine tuning of photosynthesis. This relationship between the complexity of the antenna and the increasing complexity of the organism is mainly related to the remarkable acclimation capability of complex organisms under fluctuating environmental conditions. These antenna complexes not only harvest light, but also provide photoprotection under fluctuating light conditions. In this review, the evolution, structure, and function of different antenna complexes, from single cellular organisms to higher plants, are discussed in the context of the ability to acclimate and adapt to cope under fluctuating environmental conditions.

Conserved Residues in the C-Terminal Domain Affect the Structure and Function of CYP38 in Arabidopsis

Arabidopsis cyclophilin38 (CYP38) is a thylakoid lumen protein critial for PSII assembly and maintenance, and its C-terminal region serves as the target binding domain. We hypothesized that four conserved residues (R290, F294, Q372, and F374) in the C-terminal domain are critical for the structure and function of CYP38. In yeast two-hybrid and protein pull-down assays, CYP38s with single-sited mutations (R290A, F294A, Q372A, or F374A) did not interact with the CP47 E-loop as the wild-type CYP38. In contrast, CYP38 with the R290A/F294A/Q372A/F374A quadruple mutation could bind the CP47 E-loop. Gene transformation analysis showed that the quadruple mutation prevented CYP38 to efficiently complement the mutant phenotype of cyp38. The C-terminal domain half protein with the quadruple mutation, like the wild-type one, could interact with the N-terminal domain or the CP47 E-loop in vitro. The cyp38 plants expressing CYP38 with the quadruple mutation showed a similar BN-PAGE profile as cyp38, but distinct from the wild type. The CYP38 protein with the quadruple mutation associated with the thylakoid membrane less efficiently than the wild-type CYP38. We concluded that these four conserved residues are indispensable as changes of all these residues together resulted in a subtle conformational change of CYP38 and reduced its intramolecular N-C interaction and the ability to associate with the thylakoid membrane, thus impairing its function in chloroplast.

Antenna arrangement and energy-transfer pathways of PSI-LHCI from the moss Physcomitrella patens

Plants harvest light energy utilized for photosynthesis by light-harvesting complex I and II (LHCI and LHCII) surrounding photosystem I and II (PSI and PSII), respectively. During the evolution of green plants, moss is at an evolutionarily intermediate position from aquatic photosynthetic organisms to land plants, being the first photosynthetic organisms that landed. Here, we report the structure of the PSI–LHCI supercomplex from the moss Physcomitrella patens (Pp) at 3.23 Å resolution solved by cryo-electron microscopy. Our structure revealed that four Lhca subunits are associated with the PSI core in an order of Lhca1–Lhca5–Lhca2–Lhca3. This number is much decreased from 8 to 10, the number of subunits in most green algal PSI–LHCI, but the same as those of land plants. Although Pp PSI–LHCI has a similar structure as PSI–LHCI of land plants, it has Lhca5, instead of Lhca4, in the second position of Lhca, and several differences were found in the arrangement of chlorophylls among green algal, moss, and land plant PSI–LHCI. One chlorophyll, PsaF–Chl 305, which is found in the moss PSI–LHCI, is located at the gap region between the two middle Lhca subunits and the PSI core, and therefore may make the excitation energy transfer from LHCI to the core more efficient than that of land plants. On the other hand, energy-transfer paths at the two side Lhca subunits are relatively conserved. These results provide a structural basis for unravelling the mechanisms of light-energy harvesting and transfer in the moss PSI–LHCI, as well as important clues on the changes of PSI–LHCI after landing.

The Significance of Chloroplast NAD(P)H Dehydrogenase Complex and Its Dependent Cyclic Electron Transport in Photosynthesis

Chloroplast NAD(P)H dehydrogenase (NDH) complex, a multiple-subunit complex in the thylakoid membranes mediating cyclic electron transport, is one of the most important alternative electron transport pathways. It was identified to be essential for plant growth and development during stress periods in recent years. The NDH-mediated cyclic electron transport can restore the over-reduction in stroma, maintaining the balance of the redox system in the electron transfer chain and providing the extra ATP needed for the other biochemical reactions. In this review, we discuss the research history and the subunit composition of NDH. Specifically, the formation and significance of NDH-mediated cyclic electron transport are discussed from the perspective of plant evolution and physiological functionality of NDH facilitating plants' adaptation to environmental stress. A better understanding of the NDH-mediated cyclic electron transport during photosynthesis may offer new approaches to improving crop yield.

Developmental acclimation of the thylakoid proteome to light intensity in Arabidopsis

Photosynthetic acclimation, the ability to adjust the composition of the thylakoid membrane to optimise the efficiency of electron transfer to the prevailing light conditions, is crucial to plant fitness in the field. While much is known about photosynthetic acclimation in Arabidopsis, to date there has been no study that combines both quantitative label-free proteomics and photosynthetic analysis by gas exchange, chlorophyll fluorescence and P700 absorption spectroscopy. Using these methods we investigated how the levels of 402 thylakoid proteins, including many regulatory proteins not previously quantified, varied upon long-term (weeks) acclimation of Arabidopsis to low (LL), moderate (ML) and high (HL) growth light intensity and correlated these with key photosynthetic parameters. We show that changes in the relative abundance of cytb6 f, ATP synthase, FNR2, TIC62 and PGR6 positively correlate with changes in estimated PSII electron transfer rate and CO2 assimilation. Improved photosynthetic capacity in HL grown plants is paralleled by increased cyclic electron transport, which positively correlated with NDH, PGRL1, FNR1, FNR2 and TIC62, although not PGR5 abundance. The photoprotective acclimation strategy was also contrasting, with LL plants favouring slowly reversible non-photochemical quenching (qI), which positively correlated with LCNP, while HL plants favoured rapidly reversible quenching (qE), which positively correlated with PSBS. The long-term adjustment of thylakoid membrane grana diameter positively correlated with LHCII levels, while grana stacking negatively correlated with CURT1 and RIQ protein abundance. The data provide insights into how Arabidopsis tunes photosynthetic electron transfer and its regulation during developmental acclimation to light intensity.

Composition, phosphorylation and dynamic organization of photosynthetic protein complexes in plant thylakoid membrane

The photosystems (PS), catalyzing the photosynthetic reactions of higher plants, are unevenly distributed in the thylakoid membrane: PSII, together with its light harvesting complex (LHC)II, is enriched in the appressed grana stacks, while PSI-LHCI resides in the non-appressed stroma thylakoids, which wind around the grana stacks. The two photosystems interact in a third membrane domain, the grana margins, which connect the grana and stroma thylakoids and allow the loosely bound LHCII to serve as an additional antenna for PSI. The light harvesting is balanced by reversible phosphorylation of LHCII proteins. Nevertheless, light energy also damages PSII and the repair process is regulated by reversible phosphorylation of PSII core proteins. Here, we discuss the detailed composition and organization of PSII-LHCII and PSI-LHCI (super)complexes in the thylakoid membrane of angiosperm chloroplasts and address the role of thylakoid protein phosphorylation in dynamics of the entire protein complex network of the photosynthetic membrane. Finally, we scrutinize the phosphorylation-dependent dynamics of the protein complexes in context of thylakoid ultrastructure and present a model on the reorganization of the entire thylakoid network in response to changes in thylakoid protein phosphorylation.

Effect of light on the rearrangements of PSI super-and megacomplexes in the non-appressed thylakoid domains of maize mesophyll chloroplasts

We demonstrated the existence of PSI-LHCI-LHCII-Lhcb4 supercomplexes and PSI-LHCI-PSII-LHCII megacomplexes in the stroma lamellae and grana margins of maize mesophyll chloroplasts; these complexes consist of different LHCII trimers and monomer antenna proteins per PSI photocentre. These complexes are formed in both low (LL) and high (HL) light growth conditions, but with different contents. We attempted to identify the components and structure of these complexes in maize chloroplasts isolated from the leaves of low and high light-grown plants after darkness and transition to far red (FR) light of high intensity. Exposition of plants from high and low light growth condition on FR light induces different rearrangements in the composition of super- and megacomplexes. During FR light exposure, in plants from LL, the PSI-LHCI-LHCII-Lhcb4 supercomplex dissociates into free LHCII-Lhcb4 and PSI-LHCI complexes, and these complexes associate with the PSII monomer. This process occurs differently in plants from HL. Exposition to FR light causes dissociation of both PSI-LHCI-LHCII-Lhcb4 supercomplexes and PSI-PSII megacomplexes. These results suggest a different function of super- and megacomplex organization than the classic state transitions model, which assumes that the movement of LHCII trimers in the thylakoid membraneis considered as a mechanism for balancing light absorption between the two photosystems in light stress. The behavior of the complexes described in this article does not seem to be well explained by this model, i.e., it does not seem likely that the primary purpose of these megacomplexes dynamics is to balance excitation pressure. Rather, as stated in this article, it seems to indicate a role of these complexes for PSI in excitation quenching and for PSII in turnover.

iTRAQ-based comparative proteomic analysis of differences in the protein profiles of stems and leaves from two alfalfa genotypes

BACKGROUND

To explore the molecular regulatory mechanisms of early stem and leaf development, proteomic analysis was performed on leaves and stems of F genotype alfalfa, with thin stems and small leaves, and M genotype alfalfa, with thick stems and large leaves.

RESULTS

Based on fold-change thresholds of > 1.20 or < 0.83 (p < 0.05), a large number of proteins were identified as being differentially enriched between the M and F genotypes: 249 downregulated and 139 upregulated in stems and 164 downregulated and 134 upregulated in leaves. The differentially enriched proteins in stems were mainly involved in amino acid biosynthesis, phenylpropanoid biosynthesis, carbon fixation, and phenylalanine metabolism. The differentially enriched proteins in leaves were mainly involved in porphyrin and chlorophyll metabolism, phenylpropanoid biosynthesis, starch and sucrose metabolism, and carbon fixation in photosynthetic organisms. Six differentially enriched proteins were mapped onto the porphyrin and chlorophyll metabolism pathway in leaves of the M genotype, including five upregulated proteins involved in chlorophyll biosynthesis and one downregulated protein involved in chlorophyll degradation. Eleven differentially enriched proteins were mapped onto the phenylpropanoid pathway in stems of the M genotype, including two upregulated proteins and nine downregulated proteins.

CONCLUSION

Enhanced chlorophyll synthesis and decreased lignin synthesis provided a reasonable explanation for the larger leaves and lower levels of stem lignification in M genotype alfalfa. This proteomic study aimed to classify the functions of differentially enriched proteins and to provide information on the molecular regulatory networks involved in stem and leaf development.

The chloroplast NADH dehydrogenase-like complex influences the photosynthetic activity of the moss Physcomitrella patens

Alternative electron pathways contribute to regulation of photosynthetic light reactions to adjust to metabolic demands in dynamic environments. The chloroplast NADH dehydrogenase-like (NDH) complex mediates the cyclic electron transport pathway around PSI in different cyanobacteria, algae, and plant species, but it is not fully conserved in all photosynthetic organisms. In order to assess how the physiological role of this complex changed during plant evolution, we isolated Physcomitrella patens lines knocked out for the NDHM gene that encodes a subunit fundamental for the activity of the complex. ndhm knockout mosses indicated high PSI acceptor side limitation upon abrupt changes in illumination. In P. patens, pseudo-cyclic electron transport mediated by flavodiiron proteins (FLVs) was also shown to prevent PSI over-reduction in plants exposed to light fluctuations. flva ndhm double knockout mosses had altered photosynthetic performance and growth defects under fluctuating light compared with the wild type and single knockout mutants. The results showed that while the contribution of NDH to electron transport is minor compared with FLV, NDH still participates in modulating photosynthetic activity, and it is critical to avoid PSI photoinhibition, especially when FLVs are inactive. The functional overlap between NDH- and FLV-dependent electron transport supports PSI activity and prevents its photoinhibition under light variations.

Genes encoding light-harvesting chlorophyll a/b-binding proteins in papaya (Carica papaya L.) and insight into lineage-specific evolution in Brassicaceae

Light-harvesting chlorophyll a/b-binding (Lhc) proteins comprise a plant-specific superfamily involved in photosynthesis and stress responses. Despite their importance, little is known in papaya (Carica papaya), an economically important tree fruit crop as well as a species close to the model plant arabidopsis (Arabidopsis thaliana). This study reports a first genome-wide analysis of Lhc superfamily genes in papaya, and a total of 28 members that represent four defined families or 26 orthologous groups were identified from the papaya genome. The superfamily number is comparable to 28 or 27 reported in castor (Ricinus communis) and jatropha (Jatropha curcas), respectively, two Euphorbiaceous plants also without any recent whole-genome duplication (WGD), but relatively less than 35, 34, 32, 32, 37, 30 or 32 present in cassava (Manihot esculenta), arabidopsis, A. lyrata, A. halleri, Capsella rubella, C. grandiflora, and Eutrema salsugineum, respectively, representative species having experienced one or two recent WGDs. Local duplication was shown to play a predominant role in gene expansion in papaya, castor, and jatropha, which is only confined to the Lhcb1 group. By contrast, WGD plays a relatively more important role in cassava, arabidopsis, and other Brassicaceous plants. Further comparison of Brassicaceous plants revealed that loss of the SEP6 group in arabidopsis is lineage-specific, occurring sometime after papaya-arabidopsis divergence but before the radiation of Brassicaceous plants. Transcriptional profiling revealed a leaf-preferential expression pattern of most CpLhc superfamily genes and their transcript levels were markedly regulated by three abiotic stresses, i.e., mimicking drought, cold, and high salt. These findings not only facilitate further functional studies in papaya, but also improve our knowledge on lineage-specific evolution of this special gene superfamily in Brassicaceae.

The plastid NAD(P)H dehydrogenase-like complex: structure, function and evolutionary dynamics

The thylakoid NAD(P)H dehydrogenase-like (NDH) complex is a large protein complex that reduces plastoquinone and pumps protons into the lumen generating protonmotive force. In plants, the complex consists of both nuclear and chloroplast-encoded subunits. Despite its perceived importance for stress tolerance and ATP generation, chloroplast-encoded NDH subunits have been lost numerous times during evolution in species occupying seemingly unrelated environmental niches. We have generated a phylogenetic tree that reveals independent losses in multiple phylogenetic lineages, and we use this tree as a reference to discuss possible evolutionary contexts that may have relaxed selective pressure for retention of ndh genes. While we are still yet unable to pinpoint a singular specific lifestyle that negates the need for NDH, we are able to rule out several long-standing explanations. In light of this, we discuss the biochemical changes that would be required for the chloroplast to dispense with NDH functionality with regards to known and proposed NDH-related reactions.

Recent advances on the structure and function of NDH-1: The complex I of oxygenic photosynthesis

Photosynthetic NADH dehydrogenase-like complex type-1 (a.k.a, NDH, NDH-1, or NDH-1L) is a multi-subunit, membrane-bound oxidoreductase related to the respiratory complex I. Although originally discovered 30 years ago, a number of recent advances have revealed significant insight into the structure, function, and physiology of NDH-1. Here, we highlight progress in understanding the function of NDH-1 in the photosynthetic light reactions of both cyanobacteria and chloroplasts from biochemical and structural perspectives. We further examine the cyanobacterial-specific forms of NDH-1 that possess vectorial carbonic anhydrase (vCA) activity and function in the CO₂-concentrating mechanism (CCM). We compare the proposed mechanism for the cyanobacterial NDH-1 vCA-activity to that of the DAB (DABs accumulates bicarbonate) complex, another putative vCA. Finally, we discuss both new and remaining questions pertaining to the mechanisms of NDH-1 complexes in light of these recent advances.

Structural variability, coordination and adaptation of a native photosynthetic machinery

Cyanobacterial thylakoid membranes represent the active sites for both photosynthetic and respiratory electron transport. We used high-resolution atomic force microscopy to visualize the native organization and interactions of photosynthetic complexes within the thylakoid membranes from the model cyanobacterium Synechococcus elongatus PCC 7942. The thylakoid membranes are heterogeneous and assemble photosynthetic complexes into functional domains to enhance their coordination and regulation. Under high light, the chlorophyll-binding proteins IsiA are strongly expressed and associate with Photosystem I (PSI), forming highly variable IsiA-PSI supercomplexes to increase the absorption cross-section of PSI. There are also tight interactions of PSI with Photosystem II (PSII), cytochrome b₆f, ATP synthase and NAD(P)H dehydrogenase complexes. The organizational variability of these photosynthetic supercomplexes permits efficient linear and cyclic electron transport as well as bioenergetic regulation. Understanding the organizational landscape and environmental adaptation of cyanobacterial thylakoid membranes may help inform strategies for engineering efficient photosynthetic systems and photo-biofactories.

PsbQ-Like Protein 3 Functions as an Assembly Factor for the Chloroplast NADH Dehydrogenase-Like Complex in Arabidopsis

Angiosperms have three PsbQ-like (PQL) proteins in addition to the PsbQ subunit of the oxygen-evolving complex of photosystem II. Previous studies have shown that two PQL proteins, PnsL2 and PnsL3, are subunits of the chloroplast NADH dehydrogenase-like (NDH) complex involved in the photosystem I (PSI) cyclic electron flow. In addition, another PsbQ homolog, PQL3, is required for the NDH activity; however, the molecular function of PQL3 has not been elucidated. Here, we show that PQL3 is an assembly factor, particularly for the accumulation of subcomplex B (SubB) of the chloroplast NDH. In the pql3 mutant of Arabidopsis thaliana, the amounts of NDH subunits in SubB, PnsB1 and PsnB4, were decreased, causing a severe reduction in the NDH-PSI supercomplex. Analysis using blue native polyacrylamide gel electrophoresis suggested that the incorporation of PnsL3 into SubB was affected in the pql3 mutant. Unlike other PsbQ homologs, PQL3 was weakly associated with thylakoid membranes and was only partially protected from thermolysin digestion. Consistent with the function as an assembly factor, PQL3 accumulated independently in other NDH mutants, such as pnsl1-3. Furthermore, PQL3 accumulated in young leaves in a manner similar to the accumulation of CRR3, an assembly factor for SubB. These results suggest that PQL3 has developed a distinct function as an assembly factor for the NDH complex during evolution of the PsbQ protein family in angiosperms.

Ssl3451 is Important for Accumulation of NDH-1 Assembly Intermediates in the Cytoplasm of Synechocystis sp. Strain PCC 6803

Two mutants sensitive to high light for growth and impaired in NDH-1 activity were isolated from a transposon-tagged library of Synechocystis sp. strain PCC 6803. Both mutants were tagged in the ssl3451 gene encoding a hypothetical protein, which shares a significant homology with the Arabidopsis (Arabidopsis thaliana) CHLORORESPIRATORY REDUCTION 42 (CRR42). In Arabidopsis, CRR42 associates only with an NDH-1 hydrophilic arm assembly intermediate (NAI) of about 400 kDa (NAI400), one of total three NAIs (NAI800, NAI500 and NAI400), and its deletion has little, if any, effect on accumulation of any NAIs in the stroma. In comparison, the ssl3451 product was localized mainly in the cytoplasm and associates with two NAIs of about 300 kDa (NAI300) and 130 kDa (NAI130). Deletion of Ssl3451 reduced the abundance of the NAI300 complex to levels no longer visible on gels and of the NAI130 complex to a low level, thereby impeding the assembly process of NDH-1 hydrophilic arm. Further, Ssl3451 interacts with another assembly factor Ssl3829 and they have a similar effect on accumulation of NAIs and NdhI maturation factor Slr1097 in the cytoplasm. We thus propose that Ssl3451 plays an important role in accumulation of the NAI300 and NAI130 complexes in the cytoplasm via its interacting protein Ssl3829.

Role of cyclic and pseudo-cyclic electron transport in response to dynamic light changes in Physcomitrella patens

Photosynthetic organisms support cell metabolism by harvesting sunlight and driving the electron transport chain at the level of thylakoid membranes. Excitation energy and electron flow in the photosynthetic apparatus is continuously modulated in response to dynamic environmental conditions. Alternative electron flow around photosystem I plays a seminal role in this regulation contributing to photoprotection by mitigating overreduction of the electron carriers. Different pathways of alternative electron flow coexist in the moss Physcomitrella patens, including cyclic electron flow mediated by the PGRL1/PGR5 complex and pseudo-cyclic electron flow mediated by the flavodiiron proteins FLV. In this work, we generated P. patens plants carrying both pgrl1 and flva knock-out mutations. A comparative analysis of the WT, pgrl1, flva, and pgrl1 flva lines suggests that cyclic and pseudo-cyclic processes have a synergic role in the regulation of photosynthetic electron transport. However, although both contribute to photosystem I protection from overreduction by modulating electron flow following changes in environmental conditions, FLV activity is particularly relevant in the first seconds after a light change whereas PGRL1 has a major role upon sustained strong illumination.

Isoprene Acts as a Signaling Molecule in Gene Networks Important for Stress Responses and Plant Growth

Isoprene synthase converts dimethylallyl diphosphate to isoprene and appears to be necessary and sufficient to allow plants to emit isoprene at significant rates. Isoprene can protect plants from abiotic stress but is not produced naturally by all plants; for example, Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum) do not produce isoprene. It is typically present at very low concentrations, suggesting a role as a signaling molecule; however, its exact physiological role and mechanism of action are not fully understood. We transformed Arabidopsis with a Eucalyptus globulus isoprene synthase The regulatory mechanisms of photosynthesis and isoprene emission were similar to those of native emitters, indicating that regulation of isoprene emission is not specific to isoprene-emitting species. Leaf chlorophyll and carotenoid contents were enhanced by isoprene, which also had a marked positive effect on hypocotyl, cotyledon, leaf, and inflorescence growth in Arabidopsis. By contrast, leaf and stem growth was reduced in tobacco engineered to emit isoprene. Expression of genes belonging to signaling networks or associated with specific growth regulators (e.g. gibberellic acid that promotes growth and jasmonic acid that promotes defense) and genes that lead to stress tolerance was altered by isoprene emission. Isoprene likely executes its effects on growth and stress tolerance through direct regulation of gene expression. Enhancement of jasmonic acid-mediated defense signaling by isoprene may trigger a growth-defense tradeoff leading to variations in the growth response. Our data support a role for isoprene as a signaling molecule.

The mechanism of cyclic electron flow

Apart from the canonical light-driven linear electron flow (LEF) from water to CO₂, numerous regulatory and alternative electron transfer pathways exist in chloroplasts. One of them is the cyclic electron flow around Photosystem I (CEF), contributing to photoprotection of both Photosystem I and II (PSI, PSII) and supplying extra ATP to fix atmospheric carbon. Nonetheless, CEF remains an enigma in the field of functional photosynthesis as we lack understanding of its pathway. Here, we address the discrepancies between functional and genetic/biochemical data in the literature and formulate novel hypotheses about the pathway and regulation of CEF based on recent structural and kinetic information.

Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

Studying the organization of genes within genomes across broad evolutionary timescales can advance our understanding of the evolution of traits and clades. We have used a network approach to investigate genome dynamics of mammals and angiosperms. In general, genome organization and gene microcollinearity is much more conserved in mammals than in flowering plants. We then identified the genomic outliers or “rebel genes,” within each clade. Genes that have moved are unusual for mammals, whereas highly conserved single-copy genes are exceptional for plants. How conservation and changes in synteny or fundamental differences in genome organization have contributed to the evolution of lineages could be a new scientific frontier.

A comprehensive analysis of relative gene order, or microsynteny, can provide valuable information for understanding the evolutionary history of genes and genomes, and ultimately traits and species, across broad phylogenetic groups and divergence times. We have used our network-based phylogenomic synteny analysis pipeline to first analyze the overall patterns and major differences between 87 mammalian and 107 angiosperm genomes. These two important groups have both evolved and radiated over the last ∼170 MYR. Secondly, we identified the genomic outliers or “rebel genes” within each clade. We theorize that rebel genes potentially have influenced trait and lineage evolution. Microsynteny networks use genes as nodes and syntenic relationships between genes as edges. Networks were decomposed into clusters using the Infomap algorithm, followed by phylogenomic copy-number profiling of each cluster. The differences in syntenic properties of all annotated gene families, including BUSCO genes, between the two clades are striking: most genes are single copy and syntenic across mammalian genomes, whereas most genes are multicopy and/or have lineage-specific distributions for angiosperms. We propose microsynteny scores as an alternative and complementary metric to BUSCO for assessing genome assemblies. We further found that the rebel genes are different between the two groups: lineage-specific gene transpositions are unusual in mammals, whereas single-copy highly syntenic genes are rare for flowering plants. We illustrate several examples of mammalian transpositions, such as brain-development genes in primates, and syntenic conservation across angiosperms, such as single-copy genes related to photosynthesis. Future experimental work can test if these are indeed rebels with a cause.

A Supercomplex, of Approximately 720 kDa and Composed of Both Photosystem Reaction Centers, Dissipates Excess Energy by PSI in Green Macroalgae Under Salt Stress

The thylakoid membranes of plants play a critical role in electron transfer and energy fixation, and are highly dynamic. So far, studies on the thylakoid membranes have mainly focused on microalgae and higher plants, yet very little information is available on the macroalgal thylakoids. Here, we studied the structure and organization of the thylakoid membranes in Ulva prolifera, a representative species of the green macroalgae. We found that U. prolifera had few but long loosely stacked membranes which lack the conventional grana found in higher plants. However, the thylakoid membrane complexes demonstrate lateral heterogeneity. Moreover, we found a supercomplex composed of PSII, light-harvesting complex II (LHCII) and PSI from U. prolifera under salt stress. The supercomplex is approximately 720 kDa, and includes the two important photoprotection proteins, the PSII S subunit (PsbS) and the light-harvesting complex stress-related protein (LhcSR), as well as xanthophyll cycle pigments (violaxanthin, antheraxanthin and zeaxanthin). Time-resolved fluorescence analysis suggested that, in the supercomplex, excitation energy could efficiently be transferred from PSII to PSI, even when PSII was inhibited, a function which disappeared when the supercomplex was incubated in mild detergent. We suggest that the supercomplex might be an important mechanism to dissipate excess energy by PSI in green macroalgae under salt stress.

Stepwise evolution of supercomplex formation with photosystem I is required for stabilization of chloroplast NADH dehydrogenase-like complex: Lhca5-dependent supercomplex formation in Physcomitrella patens

In angiosperms, such as Arabidopsis and barley, the chloroplast NADH dehydrogenase-like (NDH) complex associates with two copies of photosystem I (PSI) supercomplex to form an NDH-PSI supercomplex for the stabilization of the NDH complex. Two linker proteins, Lhca5 and Lhca6, are members of the light-harvesting complex I (LHCI) family and mediate this supercomplex formation. The liverwort Marchantia polymorpha has branched from the basal land plant lineage and has neither Lhca5 nor Lhca6. Consequently, the NDH complex does not form a supercomplex with PSI in this plant. The Lhca6 gene does not seem to exist also in the moss Physcomitrella patens (Physcomitrella). Conversely, the Lhca5 gene has been found in Physcomitrella, although experimental evidence is still lacking for its contribution to NDH-PSI supercomplex formation as a linker. Here, we biochemically characterized the Lhca5 knock-out mutant (lhca5) in Physcomitrella. The NDH-PSI supercomplex observed in wild-type Physcomitrella was absent in the lhca5 mutant. Lhca5 protein was detected in this NDH-PSI supercomplex. Some PSI and NDH subunits were co-immunoprecipitated with Lhca5-HA. These results indicate that the Physcomitrella gene is the functional ortholog of Lhca5 reported in Arabidopsis. Between Physcomitrella and Arabidopsis, the stromal loop region is highly conserved in Lhca5 proteins but not in other LHCI members. We found that Lhca5 contributed to the stable accumulation of the NDH complex, but part of the NDH complex was still sensitive to high light intensity, even in the wild-type. We considered that angiosperms acquired another linker protein, Lhca6, to further stabilize the NDH complex.