AtCYP38 ensures early biogenesis, correct assembly and sustenance of photosystem II

N-Phenylnorbornenesuccinimide derivatives, agricultural defensive, and enzymatic target selection

BACKGROUND

Faced with the need to develop new herbicides with modes of action different to those observed for existing agrochemicals, one of the most promising strategies employed by synthetic chemists involves the structural modification of molecules found in natural products. Molecules containing amides, imides, and epoxides as functional groups are prevalent in nature and find extensive application in synthesizing more intricate compounds due to their biological properties. In this context, this paper delineates the synthesis of N-phenylnorbornenesuccinimide derivatives, conducts biological assays, and carries out in silico investigation of the protein target associated with the most potent compound in plant organisms. The phytotoxic effects of the synthesized compounds (2-29) were evaluated on Allium cepa, Bidens pilosa, Cucumis sativus, Sorghum bicolor, and Solanum lycopersicum.

RESULTS

Reaction of endo-bicyclo[2.2.1]hept-5-ene-3a,7a-dicarboxylic anhydride (1) with aromatic amines led to the N-phenylnorbornenesuccinic acids (2-11) with yields ranging from 75% to 90%. Cyclization of compounds (2-11) in the presence of acetic anhydride and sodium acetate afforded N-phenylnorbornenesuccinimides (12-20) with yields varying from 65% to 89%. Those imides were then subjected to epoxidation reaction to afford N-phenylepoxynorbornanesuccimides (21-29) with yields from 60% to 90%. All compounds inhibited the growth of seedlings of the plants evaluated. Substance 23 was the most active against the plants tested, inhibiting 100% the growth of all species in all concentrations. Cyclophilin was found to be the enzymatic target of compound 23.

CONCLUSION

These findings suggest that derivatives of N-phenylnorbornenesuccinimide are promising compounds in the quest for more selective and stable agrochemicals. This perspective reinforces the significance of these derivatives as potential innovative herbicides and emphasizes the importance of further exploring their biological activity on weeds. © 2024 Society of Chemical Industry.

A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes

Mutant populations are crucial for functional genomics and discovering novel traits for crop breeding. Sorghum, a drought and heat-tolerant C4 species, requires a vast, large-scale, annotated, and sequenced mutant resource to enhance crop improvement through functional genomics research. Here, we report a sorghum large-scale sequenced mutant population with 9.5 million ethyl methane sulfonate (EMS)-induced mutations that covered 98% of sorghum's annotated genes using inbred line BTx623. Remarkably, a total of 610 320 mutations within the promoter and enhancer regions of 18 000 and 11 790 genes, respectively, can be leveraged for novel research of cis-regulatory elements. A comparison of the distribution of mutations in the large-scale mutant library and sorghum association panel (SAP) provides insights into the influence of selection. EMS-induced mutations appeared to be random across different regions of the genome without significant enrichment in different sections of a gene, including the 5' UTR, gene body, and 3'-UTR. In contrast, there were low variation density in the coding and UTR regions in the SAP. Based on the Ka /Ks value, the mutant library (~1) experienced little selection, unlike the SAP (0.40), which has been strongly selected through breeding. All mutation data are publicly searchable through SorbMutDB (https://www.depts.ttu.edu/igcast/sorbmutdb.php) and SorghumBase (https://sorghumbase.org/). This current large-scale sequence-indexed sorghum mutant population is a crucial resource that enriched the sorghum gene pool with novel diversity and a highly valuable tool for the Poaceae family, that will advance plant biology research and crop breeding.

Immunophilin CYN28 is required for accumulation of photosystem II and thylakoid FtsH protease in Chlamydomonas

Excess light causes severe photodamage to photosystem II (PSII) where the primary charge separation for electron transfer takes place. Dissection of mechanisms underlying the PSII maintenance and repair cycle in green algae promotes the usage of genetic engineering and synthetic biology to improve photosynthesis and biomass production. In this study, we systematically analyzed the high light (HL) responsive immunophilin genes in Chlamydomonas (Chlamydomonas reinhardtii) and identified one chloroplast lumen-localized immunophilin, CYN28, as an essential player in HL tolerance. Lack of CYN28 caused HL hypersensitivity, severely reduced accumulation of PSII supercomplexes and compromised PSII repair in cyn28. The thylakoid FtsH (filamentation temperature-sensitive H) is an essential AAA family metalloprotease involved in the degradation of photodamaged D1 during the PSII repair cycle and was identified as one potential target of CYN28. In the cyn28 mutant, the thylakoid FtsH undergoes inefficient turnover under HL conditions. The CYN28-FtsH1/2 interaction relies on the FtsH N-terminal proline residues and is strengthened particularly under HL. Further analyses demonstrated CYN28 displays peptidyl-prolyl isomerase (PPIase) activity, which is necessary for its physiological function. Taken together, we propose that immunophilin CYN28 participates in PSII maintenance and regulates the homeostasis of FtsH under HL stress via its PPIase activity.

Enhanced Carbonylation of Photosynthetic and Glycolytic Proteins in Antibiotic Timentin-Treated Tobacco In Vitro Shoot Culture

Antibiotics are used in plant in vitro tissue culture to eliminate microbial contamination or for selection in genetic transformation. Antibiotic timentin has a relatively low cytotoxic effect on plant tissue culture; however, it could induce an enduring growth-inhibiting effect in tobacco in vitro shoot culture that persists after tissue transfer to a medium without antibiotic. The effect is associated with an increase in oxidative stress injury in plant tissues. In this study, we assessed changes of reactive oxygen species accumulation, protein expression, and oxidative protein modification response associated with enduring timentin treatment-induced growth suppression in tobacco (Nicotiana tabacum L.) in vitro shoot culture. The study revealed a gradual 1.7 and 1.9-fold increase in superoxide (O₂^•−) content at the later phase of the propagation cycle for treatment control (TC) and post-antibiotic treatment (PA) shoots; however, the O₂^•− accumulation pattern was different. For PA shoots, the increase in O₂^•− concentration occurred several days earlier, resulting in 1.2 to 1.4-fold higher O₂^•− concentration compared to TC during the period following the first week of cultivation. Although no protein expression differences were detectable between the TC and PA shoots by two-dimensional electrophoresis, the increase in O₂^•− concentration in PA shoots was associated with a 1.5-fold increase in protein carbonyl modification content after one week of cultivation, and protein carbonylation analysis revealed differential modification of 26 proteoforms involved in the biological processes of photosynthesis and glycolysis. The results imply that the timentin treatment-induced oxidative stress might be implicated in nontranslational cellular redox balance regulation, accelerates the development of senescence of the shoot culture, and contributes to the shoot growth-suppressing effect of antibiotic treatment.

Transcriptome Profiling in the Marine Red Alga Neopyropia yezoensis Under Light/Dark Cycle

Many organisms are subjected to a daily cycle of light and darkness, which significantly influences metabolic and physiological processes. In the present study, Neopyropia yezoensis, one of the major cultivated seaweeds used in "nori," was harvested in the morning and evening during light/dark treatments to investigate daily changes in gene expression using RNA-sequencing. A high abundance of transcripts in the morning includes the genes associated with carbon-nitrogen assimilations, polyunsaturated fatty acid, and starch synthesis. In contrast, the upregulation of a subset of the genes associated with the pentose phosphate pathway, cell cycle, and DNA replication at evening is necessary for the tight control of light-sensitive processes, such as DNA replication. Additionally, a high abundance of transcripts at dusk encoding asparaginase and glutamate dehydrogenase imply that regulation of asparagine catabolism and tricarboxylic acid cycle possibly contributes to supply nitrogen and carbon, respectively, for growth during the dark. In addition, genes encoding cryptochrome/photolyase family and histone modification proteins were identified as potential key players for regulating diurnal rhythmic genes.

Cyclophilin anaCyp40 regulates photosystem assembly and phycobilisome association in a cyanobacterium

Cyclophilins, or immunophilins, are proteins found in many organisms including bacteria, plants and humans. Most of them display peptidyl-prolyl cis-trans isomerase activity, and play roles as chaperones or in signal transduction. Here, we show that cyclophilin anaCyp40 from the cyanobacterium Anabaena sp. PCC 7120 is enzymatically active, and seems to be involved in general stress responses and in assembly of photosynthetic complexes. The protein is associated with the thylakoid membrane and interacts with phycobilisome and photosystem components. Knockdown of anacyp40 leads to growth defects under high-salt and high-light conditions, and reduced energy transfer from phycobilisomes to photosystems. Elucidation of the anaCyp40 crystal structure at 1.2-Å resolution reveals an N-terminal helical domain with similarity to PsbQ components of plant photosystem II, and a C-terminal cyclophilin domain with a substrate-binding site. The anaCyp40 structure is distinct from that of other multi-domain cyclophilins (such as Arabidopsis thaliana Cyp38), and presents features that are absent in single-domain cyclophilins.

Characterization of the Free and Membrane-Associated Fractions of the Thylakoid Lumen Proteome in Arabidopsis thaliana

The thylakoid lumen houses proteins that are vital for photosynthetic electron transport, including water-splitting at photosystem (PS) II and shuttling of electrons from cytochrome b₆f to PSI. Other lumen proteins maintain photosynthetic activity through biogenesis and turnover of PSII complexes. Although all lumen proteins are soluble, these known details have highlighted interactions of some lumen proteins with thylakoid membranes or thylakoid-intrinsic proteins. Meanwhile, the functional details of most lumen proteins, as well as their distribution between the soluble and membrane-associated lumen fractions, remain unknown. The current study isolated the soluble free lumen (FL) and membrane-associated lumen (MAL) fractions from Arabidopsis thaliana, and used gel- and mass spectrometry-based proteomics methods to analyze the contents of each proteome. These results identified 60 lumenal proteins, and clearly distinguished the difference between the FL and MAL proteomes. The most abundant proteins in the FL fraction were involved in PSII assembly and repair, while the MAL proteome was enriched in proteins that support the oxygen-evolving complex (OEC). Novel proteins, including a new PsbP domain-containing isoform, as well as several novel post-translational modifications and N-termini, are reported, and bi-dimensional separation of the lumen proteome identified several protein oligomers in the thylakoid lumen.

Characterization of CYCLOPHILLIN38 shows that a photosynthesis-derived systemic signal controls lateral root emergence

Photosynthesis in leaves generates fixed-carbon resources and essential metabolites that support sink tissues, such as roots. Two of these metabolites, sucrose and auxin, promote growth in root systems, but the explicit connection between photosynthetic activity and control of root architecture has not been explored. Through a mutant screen to identify pathways regulating root system architecture, we identified a mutation in the Arabidopsis thaliana CYCLOPHILIN 38 (CYP38) gene, which causes accumulation of pre-emergent stage lateral roots. CYP38 was previously reported to stabilize photosystem II (PSII) in chloroplasts. CYP38 expression is enriched in shoots, and grafting experiments show that the gene acts non-cell-autonomously to promote lateral root emergence. Growth of wild-type plants under low-light conditions phenocopies the cyp38 lateral root emergence defect, as does the inhibition of PSII-dependent electron transport or Nicotinamide adenine dinucleotide phosphate (NADPH) production. Importantly, these perturbations to photosynthetic activity rapidly suppress lateral root emergence, which is separate from their effects on shoot size. Supplementary exogenous sucrose largely rescued primary root (PR) growth in cyp38, but not lateral root growth. Auxin (indole-3-acetic acid (IAA)) biosynthesis from tryptophan is dependent on reductant generated during photosynthesis. Consistently, we found that wild-type seedlings grown under low light and cyp38 mutants have highly diminished levels of IAA in root tissues. IAA treatment rescued the cyp38 lateral root defect, revealing that photosynthesis promotes lateral root emergence partly through IAA biosynthesis. These data directly confirm the importance of CYP38-dependent photosynthetic activity in supporting root growth, and define the specific contributions of two metabolites in refining root architecture under light-limited 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.

Integrated physiological and chloroplast proteome analysis of wheat seedling leaves under salt and osmotic stresses

In this study, we performed an integrated physiological and chloroplast proteome analysis of wheat seedling leaves under salt and osmotic stresses by label-free based quantitative proteomic approach. Both salt and osmotic stresses significantly increased the levels of abscisic acid and methyl jasmonate and led to damages of chloroplast ultrastructure. Main parameters of chlorophyll fluorescence and gas exchange showed a significant decline under both stresses. Quantitative proteomic analysis identified 194 and 169 chloroplast-localized differentially accumulated proteins (DAPs) responsive to salt and osmotic stresses, respectively. The abundance of main DAPs involved in light-dependent reaction were increased under salt stress, but decreased in response to osmotic stress. On the contrary, salt stress induced a significant upregulation of the DAPs associated with Calvin cycle, transcription and translation, amino acid metabolism, carbon and nitrogen metabolism, and some of them exhibited a downregulation under osmotic stress. In particular, both treatments significantly upregulated the DAPs involved in plastoglobule development, protein folding and proteolysis, hormone and vitamin synthesis. Finally, we proposed a putative synergistic responsive network of wheat chloroplast proteome under salt and osmotic stresses, aiming to provide new insights into the underlying response and defense mechanisms of wheat chloroplast proteome in response to abiotic stresses. SIGNIFICANCE: Salt and osmotic stresses are the two most common abiotic stresses that severely affect crop growth and productivity. As the main site of photosynthesis of plant cells, the chloroplast also plays important role in plant tolerance to abiotic stress. However, the response of chloroplast proteome to salt and osmotic is still poorly understood by using the traditional two-dimensional electrophoresis (2-DE) method due to a poor resolution of chloroplast protein separation and low throughput identification of differentially accumulated proteins (DAPs). In this study, we employed label-free based quantitative proteomic approach to perform an integrated physiological and large-scale chloroplast proteome analysis of wheat seedling leaves under salt and osmotic stresses, which laid a solid foundation for future studies into the response and defense mechanisms of wheat chloroplast in response to abiotic stresses.

New tools for characterizing early brown stem rot disease resistance signaling in soybean

Brown stem rot (BSR) reduces soybean [Glycine max (L.) Merr.] yield by up to 38%. The BSR causal agent is Phialophora gregata f. sp. sojae, a slow-growing, necrotrophic fungus whose life cycle includes latent and pathogenic phases, each lasting several weeks. Brown stem rot foliar symptoms are often misdiagnosed as other soybean diseases or nutrient stress, making BSR resistance especially difficult to phenotype. To shed light on the genes and networks contributing to P. gregata resistance, we conducted RNA sequencing (RNA-seq) of a resistant genotype (PI 437970, Rbs3). Leaf, stem, and root tissues were collected 12, 24, and 36 h after stab inoculation with P. gregata, or mock infection, in the plant stem. By using multiple tissues and time points, we could see that leaves, stems, and roots use the same defense pathways. Our analyses suggest that P. gregata induces a biphasic defense response, with pathogen-associated molecular pattern (PAMP) triggered immunity observed in leaves at 12 and 24 h after infection (HAI) and effector triggered immunity detected at 36 h after infection in the stems. Gene networks associated with defense, photosynthesis, nutrient homeostasis, DNA replication, and growth are the hallmarks of resistance to P. gregata. While P. gregata is a slow-growing pathogen, our results demonstrate that pathogen recognition occurs hours after infection. By exploiting the genes and networks described here, we will be able to develop novel diagnostic tools to facilitate breeding and screening for BSR resistance.

Plant Cyclophilins: Multifaceted Proteins With Versatile Roles

Cyclophilins constitute a family of ubiquitous proteins that bind cyclosporin A (CsA), an immunosuppressant drug. Several of these proteins possess peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans isomerization of the peptide bond preceding a proline residue, essential for correct folding of the proteins. Compared to prokaryotes and other eukaryotes studied until now, the cyclophilin gene families in plants exhibit considerable expansion. With few exceptions, the role of the majority of these proteins in plants is still a matter of conjecture. However, recent studies suggest that cyclophilins are highly versatile proteins with multiple functionalities, and regulate a plethora of growth and development processes in plants, ranging from hormone signaling to the stress response. The present review discusses the implications of cyclophilins in different facets of cellular processes, particularly in the context of plants, and provides a glimpse into the molecular mechanisms by which these proteins fine-tune the diverse physiological pathways.

A Brassica napus Reductase Gene Dissected by Associative Transcriptomics Enhances Plant Adaption to Freezing Stress

Cold treatment (vernalization) is required for winter crops such as rapeseed (Brassica napus L.). However, excessive exposure to low temperature (LT) in winter is also a stress for the semi-winter, early-flowering rapeseed varieties widely cultivated in China. Photosynthetic efficiency is one of the key determinants, and thus a good indicator for LT tolerance in plants. So far, the genetic basis underlying photosynthetic efficiency is poorly understood in rapeseed. Here the current study used Associative Transcriptomics to identify genetic loci controlling photosynthetic gas exchange parameters in a diversity panel comprising 123 accessions. A total of 201 significant Single Nucleotide Polymorphisms (SNPs) and 147 Gene Expression Markers (GEMs) were detected, leading to the identification of 22 candidate genes. Of these, Cab026133.1, an ortholog of the Arabidopsis gene AT2G29300.2 encoding a tropinone reductase (BnTR1), was further confirmed to be closely linked to transpiration rate. Ectopic expressing BnTR1 in Arabidopsis plants significantly increased the transpiration rate and enhanced LT tolerance under freezing conditions. Also, a much higher level of alkaloids content was observed in the transgenic Arabidopsis plants, which could help protect against LT stress. Together, the current study showed that AT is an effective approach for dissecting LT tolerance trait in rapeseed and that BnTR1 is a good target gene for the genetic improvement of LT tolerance in plant.

Exploring the proteome associated with the mRNA encoding the D1 reaction center protein of Photosystem II in plant chloroplasts

Synthesis of the D1 reaction center protein of Photosystem II is dynamically regulated in response to environmental and developmental cues. In chloroplasts, much of this regulation occurs at the post-transcriptional level, but the proteins responsible are largely unknown. To discover proteins that impact psbA expression, we identified proteins that associate with maize psbA mRNA by: (i) formaldehyde cross-linking of leaf tissue followed by antisense oligonucleotide affinity capture of psbA mRNA; and (ii) co-immunoprecipitation with HCF173, a psbA translational activator that is known to bind psbA mRNA. The S1 domain protein SRRP1 and two RNA Recognition Motif (RRM) domain proteins, CP33C and CP33B, were enriched with both approaches. Orthologous proteins were also among the enriched protein set in a previous study in Arabidopsis that employed a designer RNA-binding protein as a psbA RNA affinity tag. We show here that CP33B is bound to psbA mRNA in vivo, as was shown previously for CP33C and SRRP1. Immunoblot, pulse labeling, and ribosome profiling analyses of mutants lacking CP33B and/or CP33C detected some decreases in D1 protein levels under some conditions, but no change in psbA RNA abundance or translation. However, analogous experiments showed that SRRP1 represses psbA ribosome association in the dark, represses ycf1 ribosome association, and promotes accumulation of ndhC mRNA. As SRRP1 is known to harbor RNA chaperone activity, we postulate that SRRP1 mediates these effects by modulating RNA structures. The uncharacterized proteins that emerged from our analyses provide a resource for the discovery of proteins that impact the expression of psbA and other chloroplast genes.

Complex lumenal immunophilin AtCYP38 influences thylakoid remodelling in Arabidopsis thaliana

Investigations of the luminal immunophilin AtCYP38 (cyclophilin 38) in Arabidopsis thaliana (At), the orthologue of the complex immunophilin TLP40 from Spinacia oleracea, revealed its involvement in photosystem II (PSII) repair and assembly, biogenesis of PSII complex, and cellular signalling. However, the main physiological roles of AtCYP38 and TLP40 are related to regulation of thylakoid PP2A-type phosphatase involved in PSII core protein dephosphorylation, and chaperone function during protein folding. Here we further investigate physiological roles of AtCYP38 and analyse the ultrastructure of chloroplasts from cyp38-2 plants. Transmission electron microscopy followed by quantitative micrography revealed modifications in thylakoid stacking. We also confirm that the depletion of AtCYP38 influences PSII performance, which leads to stunted phenotype of cyp38-2 plants.

Photosystem II oxygen-evolving complex photoassembly displays an inverse H/D solvent isotope effect under chloride-limiting conditions

Metal clusters play important roles in a wide variety of proteins. In cyanobacteria, algae, and plants, photosystem II uses light energy to oxidize water and release O₂ at an active site that contains 1 calcium and 4 manganese atoms. This cluster must be built within the protein environment through a process known as photoassembly. Through experiments and simulations, we found that the efficiency of photoassembly was highly dependent on protons and chloride. Surprisingly, when the solvent was switched from H₂O to deuterated water, D₂O, the yield of photoassembly was higher. These results provide insights into the stepwise mechanism of photoassembly that can inform synthesis and repair strategies being developed for artificial photosynthesis technologies.

Photosystem II (PSII) performs the solar-driven oxidation of water used to fuel oxygenic photosynthesis. The active site of water oxidation is the oxygen-evolving complex (OEC), a Mn₄CaO₅ cluster. PSII requires degradation of key subunits and reassembly of the OEC as frequently as every 20 to 40 min. The metals for the OEC are assembled within the PSII protein environment via a series of binding events and photochemically induced oxidation events, but the full mechanism is unknown. A role of proton release in this mechanism is suggested here by the observation that the yield of in vitro OEC photoassembly is higher in deuterated water, D₂O, compared with H₂O when chloride is limiting. In kinetic studies, OEC photoassembly shows a significant lag phase in H₂O at limiting chloride concentrations with an apparent H/D solvent isotope effect of 0.14 ± 0.05. The growth phase of OEC photoassembly shows an H/D solvent isotope effect of 1.5 ± 0.2. We analyzed the protonation states of the OEC protein environment using classical Multiconformer Continuum Electrostatics. Combining experiments and simulations leads to a model in which protons are lost from amino acid that will serve as OEC ligands as metals are bound. Chloride and D₂O increase the proton affinities of key amino acid residues. These residues tune the binding affinity of Mn^2+/3+ and facilitate the deprotonation of water to form a proposed μ-hydroxo bridged Mn²⁺Mn³⁺ intermediate.

Mg-dechelatase is involved in the formation of photosystem II but not in chlorophyll degradation in Chlamydomonas reinhardtii

The STAY-GREEN (SGR) gene encodes Mg-dechelatase which catalyzes the conversion of chlorophyll (Chl) a to pheophytin (Pheo) a. This reaction is the first and most important regulatory step in the Chl degradation pathway. Conversely, Pheo a is an indispensable molecule in photosystem (PS) II, suggesting the involvement of SGR in the formation of PSII. To investigate the physiological functions of SGR, we isolated Chlamydomonas sgr mutants by screening an insertion-mutant library. The sgr mutants had reduced maximum quantum efficiency of PSII (F_v /F_m ) and reduced Pheo a levels. These phenotypes were complemented by the introduction of the Chlamydomonas SGR gene. Blue Native polyacrylamide gel electrophoresis and immunoblotting analysis showed that although PSII levels were reduced in the sgr mutants, PSI and light-harvesting Chl a/b complex levels were unaffected. Under nitrogen starvation conditions, Chl degradation proceeded in the sgr mutants as in the wild type, indicating that ChlamydomonasSGR is not required for Chl degradation and primarily contributes to the formation of PSII. In contrast, in the Arabidopsis sgr triple mutant (sgr1 sgr2 sgrL), which completely lacks SGR activity, PSII was synthesized normally. These results suggest that the Arabidopsis SGR participates in Chl degradation while the ChlamydomonasSGR participates in PSII formation despite having the same catalytic property.

Versatility of Cyclophilins in Plant Growth and Survival: A Case Study in Arabidopsis

Cyclophilins (CYPs) belong to a peptidyl-prolyl cis-trans isomerase family, and were first characterized in mammals as a target of an immunosuppressive drug, cyclosporin A, preventing proinflammatory cytokine production. In Arabidopsis, 29 CYPs and CYP-like proteins are found across all subcellular compartments, involved in various physiological processes including transcriptional regulation, organogenesis, photosynthetic and hormone signaling pathways, stress adaptation and defense responses. These important but diverse activities of CYPs must be reflected by their versatility as cellular and molecular modulators. However, our current knowledge regarding their mode of actions is still far from complete. This review will briefly revisit recent progresses on the roles and mechanisms of CYPs in Arabidopsis studies, and information gaps within, which help understanding the phenotypic and environmental plasticity of plants.

Omics approaches revealed how arbuscular mycorrhizal symbiosis enhances yield and resistance to leaf pathogen in wheat

Besides improved mineral nutrition, plants colonised by arbuscular mycorrhizal (AM) fungi often display increased biomass and higher tolerance to biotic and abiotic stresses. Notwithstanding the global importance of wheat as an agricultural crop, its response to AM symbiosis has been poorly investigated. We focused on the role of an AM fungus on mineral nutrition of wheat, and on its potential protective effect against Xanthomonas translucens. To address these issues, phenotypical, molecular and metabolomic approaches were combined. Morphological observations highlighted that AM wheat plants displayed an increased biomass and grain yield, as well as a reduction in lesion area following pathogen infection. To elucidate the molecular mechanisms underlying the mycorrhizal phenotype, we investigated changes of transcripts and proteins in roots and leaves during the double (wheat-AM fungus) and tripartite (wheat-AM fungus-pathogen) interaction. Transcriptomic and proteomic profiling identified the main pathways involved in enhancing plant biomass, mineral nutrition and in promoting the bio-protective effect against the leaf pathogen. Mineral and amino acid contents in roots, leaves and seeds, and protein oxidation profiles in leaves, supported the omics data, providing new insight into the mechanisms exerted by AM symbiosis to confer stronger productivity and enhanced resistance to X. translucens in wheat.

Histological, Physiological, and Comparative Proteomic Analyses Provide Insights into Leaf Rolling in Brassica napus

Moderate leaf rolling is important in ideotype breeding, as it improves photosynthetic efficiency and therefore increases crop yields. To understand the regulatory network of leaf rolling in Brassica napus, a down-curved leaf mutant ( Bndcl1) has been investigated. Physiological analyses indicated that the chlorophyll contents and antioxidant enzyme activities were remarkably increased and the photosynthetic performance was significantly improved in Bndcl1. Consistent with these findings, 943 differentially accumulated proteins (DAPs) were identified in the Bndcl1 mutant and its wild-type plants using iTRAQ-based comparative proteomic analyses. Enrichment analysis of proteins with higher abundance in Bndcl1 revealed that the functional category "photosynthesis" was significantly overrepresented. Moreover, proteins associated with oxidative stress response and photosystem II repairing were also up-accumulated in Bndcl1, which might help the mutant to sustain the photosynthetic efficiency under unfavorable conditions. Histological observation showed that the mutant displayed defects in adaxial-abaxial patterning. Important DAPs associated with leaf polarity establishment were detected in Bndcl1, including ribosomal proteins, proteins involved in post-transcriptional gene silencing, and proteins related to brassinosteroid. Together, our findings may help clarify the mechanisms underlying leaf rolling and its physiological effects on plants and may facilitate ideotype breeding in Brassica napus.

A chloroplast thylakoid lumen protein is required for proper photosynthetic acclimation of plants under fluctuating light environments

Despite our increasingly sophisticated understanding of mechanisms ensuring efficient photosynthesis under laboratory-controlled light conditions, less is known about the regulation of photosynthesis under fluctuating light. This is important because-in nature-photosynthetic organisms experience rapid and extreme changes in sunlight, potentially causing deleterious effects on photosynthetic efficiency and productivity. Here we report that the chloroplast thylakoid lumenal protein MAINTENANCE OF PHOTOSYSTEM II UNDER HIGH LIGHT 2 (MPH2; encoded by At4g02530) is required for growth acclimation of Arabidopsis thaliana plants under controlled photoinhibitory light and fluctuating light environments. Evidence is presented that mph2 mutant light stress susceptibility results from a defect in photosystem II (PSII) repair, and our results are consistent with the hypothesis that MPH2 is involved in disassembling monomeric complexes during regeneration of dimeric functional PSII supercomplexes. Moreover, mph2-and previously characterized PSII repair-defective mutants-exhibited reduced growth under fluctuating light conditions, while PSII photoprotection-impaired mutants did not. These findings suggest that repair is not only required for PSII maintenance under static high-irradiance light conditions but is also a regulatory mechanism facilitating photosynthetic adaptation under fluctuating light environments. This work has implications for improvement of agricultural plant productivity through engineering PSII repair.

Bioinformatic and expression analysis of the Brassica napus L. cyclophilins

Cyclophilins (CYPs) are a group of ubiquitous proteins characterized by their ability to bind to the immunosuppressive drug cyclosporin A. The CYP family occurs in a wide range of organisms and contains a conserved peptidyl-prolyl cis/trans isomerase domain. In addition to fulfilling a basic role in protein folding, CYPs may also play diverse important roles, e.g. in protein degradation, mRNA processing, development, and stress responses. We performed a genome-wide database survey and identified a total of 94 CYP genes encoding 91 distinct proteins. Sequence alignment analysis of the putative BnCYP cyclophilin-like domains revealed highly conserved motifs. By using RNA-Seq, we could verify the presence of 77 BnCYP genes under control conditions. To identify phloem-specific BnCYP proteins in a complementary approach, we used LC-MS/MS to determine protein abundances in leaf and phloem extracts. We detected 26 BnCYPs in total with 12 being unique to phloem sap. Our analysis provides the basis for future studies concentrating on the functional characterization of individual members of this gene family in a plant of dual importance: as a crop and a model system for polyploidization and long-distance signalling.

Characterization of the Arabidopsis thaliana 2-Cys peroxiredoxin interactome

Peroxiredoxins are ubiquitous thiol-dependent peroxidases for which chaperone and signaling roles have been reported in various types of organisms in recent years. In plants, the peroxidase function of the two typical plastidial 2-Cys peroxiredoxins (2-Cys PRX A and B) has been highlighted while the other functions, particularly in ROS-dependent signaling pathways, are still elusive notably due to the lack of knowledge of interacting partners. Using an ex vivo approach based on co-immunoprecipitation of leaf extracts from Arabidopsis thaliana wild-type and mutant plants lacking 2-Cys PRX expression followed by mass spectrometry-based proteomics, 158 proteins were found associated with 2-Cys PRXs. Already known partners like thioredoxin-related electron donors (Chloroplastic Drought-induced Stress Protein of 32kDa, Atypical Cysteine Histidine-rich Thioredoxin 2) and enzymes involved in chlorophyll synthesis (Protochlorophyllide OxidoReductase B) or carbon metabolism (Fructose-1,6-BisPhosphatase) were identified, validating the relevance of the approach. Bioinformatic and bibliographic analyses allowed the functional classification of the identified proteins and revealed that more than 40% are localized in plastids. The possible roles of plant 2-Cys PRXs in redox signaling pathways are discussed in relation with the functions of the potential partners notably those involved in redox homeostasis, carbon and amino acid metabolisms as well as chlorophyll biosynthesis.

Revisiting the photosystem II repair cycle

The ability of photosystem (PS) II to catalyze the light-driven oxidation of water comes along with its vulnerability to oxidative damage, in particular of the D1 core subunit. Photodamaged PSII undergoes repair in a multi-step process involving (i) reversible phosphorylation of PSII core subunits; (ii) monomerization and lateral migration of the PSII core from grana to stroma thylakoids; (iii) partial disassembly of PSII; (iv) proteolytic degradation of damaged D1; (v) replacement of damaged D1 protein with a new copy; (vi) reassembly of PSII monomers and migration back to grana thylakoids for dimerization and supercomplex assembly. Here we review the current knowledge on the PSII repair cycle.

Redox regulation in the thylakoid lumen

Higher plants need to balance the efficiency of light energy absorption and dissipative photo-protection when exposed to fluctuations in light quantity and quality. This aim is partially realized through redox regulation within the chloroplast, which occurs in all chloroplast compartments except the envelope intermembrane space. In contrast to the chloroplast stroma, less attention has been paid to the thylakoid lumen, an inner, continuous space enclosed by the thylakoid membrane in which redox regulation is also essential for photosystem biogenesis and function. This sub-organelle compartment contains at least 80 lumenal proteins, more than 30 of which are known to contain disulfide bonds. Thioredoxins (Trx) in the chloroplast stroma are photo-reduced in the light, transferring reducing power to the proteins in the thylakoid membrane and ultimately the lumen through a trans-thylakoid membrane-reduced, equivalent pathway. The discovery of lumenal thiol oxidoreductase highlights the importance of the redox regulation network in the lumen for controlling disulfide bond formation, which is responsible for protein activity and folding and even plays a role in photo-protection. In addition, many lumenal members involved in photosystem assembly and non-photochemical quenching are likely required for reduction and/or oxidation to maintain their proper efficiency upon changes in light intensity. In light of recent findings, this review summarizes the multiple redox processes that occur in the thylakoid lumen in great detail, highlighting the essential auxiliary roles of lumenal proteins under fluctuating light conditions.

Chloroplast immunophilins

Immunophilins occur in almost all living organisms. They are ubiquitously expressed proteins including cyclophilins, FK506/rapamycin-binding proteins, and parvulins. Their functional significance in vascular plants is mostly related to plant developmental processes, signalling, and regulation of photosynthesis. Enzymatically active immunophilins catalyse isomerization of proline imidic peptide bonds and assist in rapid folding of nascent proline-containing polypeptides. They also participate in protein trafficking and assembly of supramolecular protein complexes. Complex immunophilins possess various additional functional domains associated with a multitude of molecular interactions. A considerable number of immunophilins act as auxiliary and/or regulatory proteins in highly specialized cellular compartments, such as lumen of thylakoids. In this review, we present a comprehensive overview of so far identified chloroplast immunophilins that assist in specific assembly/repair processes necessary for the maintenance of efficient photosynthetic energy conversion.

Overexpression of OsCYP19-4 increases tolerance to cold stress and enhances grain yield in rice (Oryza sativa)

AtCYP19-4 (also known as CYP5) was previously identified as interacting in vitro with GNOM, a member of a large family of ARF guanine nucleotide exchange factors that is required for proper polar localization of the auxin efflux carrier PIN1. The present study demonstrated that OsCYP19-4, a gene encoding a putative homologue of AtCYP19-4, was up-regulated by several stresses and showed over 10-fold up-regulation in response to cold. The study further demonstrated that the promoter of OsCYP19-4 was activated in response to cold stress. An OsCYP19-4-GFP fusion protein was targeted to the outside of the plasma membrane via the endoplasmic reticulum as determined using brefeldin A, a vesicle trafficking inhibitor. An in vitro assay with a synthetic substrate oligomer confirmed that OsCYP19-4 had peptidyl-prolyl cis-trans isomerase activity, as was previously reported for AtCYP19-4. Rice plants overexpressing OsCYP19-4 showed cold-resistance phenotypes with significantly increased tiller and spike numbers, and consequently enhanced grain weight, compared with wild-type plants. Based on these results, the authors suggest that OsCYP19-4 is required for developmental acclimation to environmental stresses, especially cold. Furthermore, the results point to the potential of manipulating OsCYP19-4 expression to enhance cold tolerance or to increase biomass.

Quality Control of Photosystem II: The Mechanisms for Avoidance and Tolerance of Light and Heat Stresses are Closely Linked to Membrane Fluidity of the Thylakoids

When oxygenic photosynthetic organisms are exposed to excessive light and/or heat, Photosystem II is damaged and electron transport is blocked. In these events, reactive oxygen species, endogenous radicals and lipid peroxidation products generated by photochemical reaction and/or heat cause the damage. Regarding light stress, plants first dissipate excessive light energy captured by light-harvesting chlorophyll protein complexes as heat to avoid the hazards, but once light stress is unavoidable, they tolerate the stress by concentrating damage in a particular protein in photosystem II, i.e., the reaction-center binding D1 protein of Photosystem II. The damaged D1 is removed by specific proteases and replaced with a new copy produced through de novo synthesis (reversible photoinhibition). When light intensity becomes extremely high, irreversible aggregation of D1 occurs and thereby D1 turnover is prevented. Once the aggregated products accumulate in Photosystem II complexes, removal of them by proteases is difficult, and irreversible inhibition of Photosystem II takes place (irreversible photoinhibition). Important is that various aspects of both the reversible and irreversible photoinhibition are highly dependent on the membrane fluidity of the thylakoids. Heat stress-induced inactivation of photosystem II is an irreversible process, which may be also affected by the fluidity of the thylakoid membranes. Here I describe why the membrane fluidity is a key to regulate the avoidance and tolerance of Photosystem II on environmental stresses.

Identification and Roles of Photosystem II Assembly, Stability, and Repair Factors in Arabidopsis

Photosystem II (PSII) is a multi-component pigment-protein complex that is responsible for water splitting, oxygen evolution, and plastoquinone reduction. Components of PSII can be classified into core proteins, low-molecular-mass proteins, extrinsic oxygen-evolving complex (OEC) proteins, and light-harvesting complex II proteins. In addition to these PSII subunits, more than 60 auxiliary proteins, enzymes, or components of thylakoid protein trafficking/targeting systems have been discovered to be directly or indirectly involved in de novo assembly and/or the repair and reassembly cycle of PSII. For example, components of thylakoid-protein-targeting complexes and the chloroplast-vesicle-transport system were found to deliver PSII subunits to thylakoid membranes. Various auxiliary proteins, such as PsbP-like (Psb stands for PSII) and light-harvesting complex-like proteins, atypical short-chain dehydrogenase/reductase family proteins, and tetratricopeptide repeat proteins, were discovered to assist the de novo assembly and stability of PSII and the repair and reassembly cycle of PSII. Furthermore, a series of enzymes were discovered to catalyze important enzymatic steps, such as C-terminal processing of the D1 protein, thiol/disulfide-modulation, peptidylprolyl isomerization, phosphorylation and dephosphorylation of PSII core and antenna proteins, and degradation of photodamaged PSII proteins. This review focuses on the current knowledge of the identities and molecular functions of different types of proteins that influence the assembly, stability, and repair of PSII in the higher plant Arabidopsis thaliana.

Analysis of photosystem II biogenesis in cyanobacteria

Photosystem II (PSII), a large multisubunit membrane protein complex found in the thylakoid membranes of cyanobacteria, algae and plants, catalyzes light-driven oxygen evolution from water and reduction of plastoquinone. Biogenesis of PSII requires coordinated assembly of at least 20 protein subunits, as well as incorporation of various organic and inorganic cofactors. The stepwise assembly process is facilitated by numerous protein factors that have been identified in recent years. Further analysis of this process requires the development or refinement of specific methods for the identification of novel assembly factors and, in particular, elucidation of the unique role of each. Here we summarize current knowledge of PSII biogenesis in cyanobacteria, focusing primarily on the impact of methodological advances and innovations. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Conrad Mullineaux.

A land plant-specific thylakoid membrane protein contributes to photosystem II maintenance in Arabidopsis thaliana

The structure and function of photosystem II (PSII) are highly susceptible to photo-oxidative damage induced by high-fluence or fluctuating light. However, many of the mechanistic details of how PSII homeostasis is maintained under photoinhibitory light remain to be determined. We describe an analysis of the Arabidopsis thaliana gene At5g07020, which encodes an unannotated integral thylakoid membrane protein. Loss of the protein causes altered PSII function under high-irradiance light, and hence it is named 'Maintenance of PSII under High light 1' (MPH1). The MPH1 protein co-purifies with PSII core complexes and co-immunoprecipitates core proteins. Consistent with a role in PSII structure, PSII complexes (supercomplexes, dimers and monomers) of the mph1 mutant are less stable in plants subjected to photoinhibitory light. Accumulation of PSII core proteins is compromised under these conditions in the presence of translational inhibitors. This is consistent with the hypothesis that the mutant has enhanced PSII protein damage rather than defective repair. These data are consistent with the distribution of the MPH1 protein in grana and stroma thylakoids, and its interaction with PSII core complexes. Taken together, these results strongly suggest a role for MPH1 in the protection and/or stabilization of PSII under high-light stress in land plants.

Translational regulation in chloroplasts for development and homeostasis

Chloroplast genomes encode 100-200 proteins which function in photosynthesis, the organellar genetic system, and other pathways and processes. These proteins are synthesized by a complete translation system within the chloroplast, with bacterial-type ribosomes and translation factors. Here, we review translational regulation in chloroplasts, focusing on changes in translation rates which occur in response to requirements for proteins encoded by the chloroplast genome for development and homeostasis. In addition, we delineate the developmental and physiological contexts and model organisms in which translational regulation in chloroplasts has been studied. This article is part of a Special Issue entitled: Chloroplast biogenesis.

Photosystem II repair in plant chloroplasts--Regulation, assisting proteins and shared components with photosystem II biogenesis

Photosystem (PS) II is a multisubunit thylakoid membrane pigment-protein complex responsible for light-driven oxidation of water and reduction of plastoquinone. Currently more than 40 proteins are known to associate with PSII, either stably or transiently. The inherent feature of the PSII complex is its vulnerability in light, with the damage mainly targeted to one of its core proteins, the D1 protein. The repair of the damaged D1 protein, i.e. the repair cycle of PSII, initiates in the grana stacks where the damage generally takes place, but subsequently continues in non-appressed thylakoid domains, where many steps are common for both the repair and de novo assembly of PSII. The sequence of the (re)assembly steps of genuine PSII subunits is relatively well-characterized in higher plants. A number of novel findings have shed light into the regulation mechanisms of lateral migration of PSII subcomplexes and the repair as well as the (re)assembly of the complex. Besides the utmost importance of the PSII repair cycle for the maintenance of PSII functionality, recent research has pointed out that the maintenance of PSI is closely dependent on regulation of the PSII repair cycle. This review focuses on the current knowledge of regulation of the repair cycle of PSII in higher plant chloroplasts. Particular emphasis is paid on sequential assembly steps of PSII and the function of the number of PSII auxiliary proteins involved both in the biogenesis and repair of PSII. This article is part of a Special Issue entitled: Chloroplast Biogenesis.

ROS-mediated enhanced transcription of CYP38 promotes the plant tolerance to high light stress by suppressing GTPase activation of PsbO2

As a member of the Immunophilin family, cyclophilin38 (CYP38) is discovered to be localized in the thylakoid lumen, and is reported to be a participant in the function regulation of thylakoid membrane protein. However, the molecule mechanisms remain unclear. We found that, CYP38 plays an important role in the process of regulating and protecting the plant to resist high light (HL) stress. Under HL condition, the gene expression of CYP38 is enhanced, and if CYP38 gene is deficient, photochemistry efficiency, and chlorophyll content falls distinctly, and excessive reactive oxygen species synthesis occurs in the chloroplast. Western blot results showed that the D1 degradation rate of cyp38 mutant plants is faster than that of wide type plants. Interestingly, both gene expression and activity of PsbO2 were drastically enhanced in cyp38 mutant plants and less changed when the deleted gene of CYP38 was restored under HL treatment. This indicates that CYP38 may impose a negative regulation effect on PsbO2, which exerts a positive regulation effect in facilitating the dephosphorylation and subsequent degradation of D1. It is also found that, under HL condition, the cytoplasmic calcium ([Ca(2+)]cyt) concentration and the gene expression level of calmodulin 3 (CaM3) arose markedly, which occurs upstream of CYP38 gene expression. In conclusion, our results indicate that CYP38 plays an important role in plant strengthening HL resistibility, which provides a new insight in the research of mechanisms of CYP38 protein in plants.

Plant immunophilins: a review of their structure-function relationship

BACKGROUND

Originally discovered as receptors for immunosuppressive drugs, immunophilins consist of two major groups, FK506 binding proteins (FKBPs) and cyclosporin A binding proteins (cyclophilins, CYPs). Many members in both FKBP and CYP families are peptidyl prolyl isomerases that are involved in protein folding processes, though they share little sequence homology. It is not surprising to find immunophilins in all organisms examined so far, including viruses, bacteria, fungi, plants and animals, as protein folding represents a common process in all living systems.

SCOPE OF REVIEW

Studies on plant immunophilins have revealed new functions beyond protein folding and new structural properties beyond that of typical PPIases. This review focuses on the structural and functional diversity of plant FKBPs and CYPs.

MAJOR CONCLUSIONS

The differences in sequence, structure as well as subcellular localization, have added on to the diversity of this family of molecular chaperones. In particular, the large number of immunophilins present in the thylakoid lumen of the photosynthetic organelle, promises to deliver insights into the regulation of photosynthesis, a unique feature of plant systems. However, very little structural information and functional data are available for plant immunophilins.

GENERAL SIGNIFICANCE

Studies on the structure and function of plant immunophilins are important in understanding their role in plant biology. By reviewing the structural and functional properties of some immunophilins that represent the emerging area of research in plant biology, we hope to increase the interest of researchers in pursuing further research in this area. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.

The PsbP and PsbQ family proteins in the photosynthetic machinery of chloroplasts

The PsbP and PsbQ proteins are extrinsic subunits of the photosystem II in eukaryotic photosynthetic organisms including higher plants, green algae and euglena. It has been suggested that PsbP and PsbQ have evolved from their cyanobacterial homologs, while considerable genetic and functional modifications have occurred to generate the eukaryote-type proteins. In addition, number of PsbP and PsbQ homologs exist in the thylakoid lumen of chloroplasts. These homologs are nuclear-encoded and likely diverged by gene duplication, and recent studies have elucidated their various functions in the photosynthetic machinery. In this short review, recent findings and new idea about these components will be discussed.

Chloroplast evolution, structure and functions

In this review, we consider a selection of recent advances in chloroplast biology. These include new findings concerning chloroplast evolution, such as the identification of Chlamydiae as a third partner in primary endosymbiosis, a second instance of primary endosymbiosis represented by the chromatophores found in amoebae of the genus Paulinella, and a new explanation for the longevity of captured chloroplasts (kleptoplasts) in sacoglossan sea slugs. The controversy surrounding the three-dimensional structure of grana, its recent resolution by tomographic analyses, and the role of the CURVATURE THYLAKOID1 (CURT1) proteins in supporting grana formation are also discussed. We also present an updated inventory of photosynthetic proteins and the factors involved in the assembly of thylakoid multiprotein complexes, and evaluate findings that reveal that cyclic electron flow involves NADPH dehydrogenase (NDH)- and PGRL1/PGR5-dependent pathways, both of which receive electrons from ferredoxin. Other topics covered in this review include new protein components of nucleoids, an updated inventory of the chloroplast proteome, new enzymes in chlorophyll biosynthesis and new candidate messengers in retrograde signaling. Finally, we discuss the first successful synthetic biology approaches that resulted in chloroplasts in which electrons from the photosynthetic light reactions are fed to enzymes derived from secondary metabolism.

AtFKBP16-1, a chloroplast lumenal immunophilin, mediates response to photosynthetic stress by regulating PsaL stability

Arabidopsis contains 16 putative chloroplast lumen-targeted immunophilins (IMMs). Proteomic analysis has enabled the subcellular localization of IMMs experimentally, but the exact biological and physiological roles of most luminal IMMs remain to be discovered. FK506-binding protein (FKBP) 16-1, one of the lumenal IMMs containing poorly conserved amino acid residues for peptidyl-prolyl isomerase (PPIase) activity, was shown to play a possible role in chloroplast biogenesis in Arabidopsis, and was also found to interact with PsaL in wheat. In this study, further evidence is provided for the notion that Arabidopsis FKBP16-1 (AtFKBP16-1) is transcriptionally and post-transcriptionally regulated by environmental stresses including high light (HL) intensity, and that overexpression of AtFKBP16-1 plants exhibited increased photosynthetic stress tolerance. A blue native-polyacrylamide gel electrophoresis/two-dimensional (BN-PAGE/2-D) analysis revealed that the increase of AtFKBP16-1 affected the levels of photosystem I (PSI)-light harvesting complex I (LHCI) and PSI-LHCI-light harvesting complex II (LHCII) supercomplex, and consequently enhanced tolerance under conditions of HL stress. In addition, plants overexpressing AtFKBP16-1 showed increased accumulation of PsaL protein and enhanced drought tolerance. Using a protease protection assay, AtFKBP16-1 protein was found to have a role in PsaL stability. The AtPsaL levels also responded to abiotic stresses derived from drought, and from methyl viologen stresses in wild-type plants. Taken together, these results suggest that AtFKBP16-1 plays a role in the acclimation of plants under photosynthetic stress conditions, probably by regulating PsaL stability.

The Arabidopsis Tellurite resistance C protein together with ALB3 is involved in photosystem II protein synthesis

Assembly of photosystem II (PSII) occurs sequentially and requires several auxiliary proteins, such as ALB3 (ALBINO3). Here, we describe the role of the Arabidopsis thaliana thylakoid membrane protein Tellurite resistance C (AtTerC) in this process. Knockout of AtTerC was previously shown to be seedling-lethal. This phenotype was rescued by expressing TerC fused C-terminally to GFP in the terc-1 background, and the resulting terc-1TerC- GFP line and an artificial miRNA-based knockdown allele (amiR-TerC) were used to analyze the TerC function. The alterations in chlorophyll fluorescence and thylakoid ultrastructure observed in amiR-TerC plants and terc-1TerC- GFP were attributed to defects in PSII. We show that this phenotype resulted from a reduction in the rate of de novo synthesis of PSII core proteins, but later steps in PSII biogenesis appeared to be less affected. Yeast two-hybrid assays showed that TerC interacts with PSII proteins. In particular, its interaction with the PSII assembly factor ALB3 has been demonstrated by co-immunoprecipitation. ALB3 is thought to assist in incorporation of CP43 into PSII via interaction with Low PSII Accumulation2 (LPA2) Low PSII Accumulation3 (LPA3). Homozygous lpa2 mutants expressing amiR-TerC displayed markedly exacerbated phenotypes, leading to seedling lethality, indicating an additive effect. We propose a model in which TerC, together with ALB3, facilitates de novo synthesis of thylakoid membrane proteins, for instance CP43, at the membrane insertion step.

Proteomic analysis of non-heading Chinese cabbage infected with Hyaloperonospora parasitica

Downy mildew is a serious fungal disease in non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) that is caused by Hyaloperonospora parasitica, which infects members of the Brassicaceae family. For breeding improvement, researchers must understand the defence mechanisms employed by non-heading Chinese cabbage to combat H. parasitica infection. Using 2-DE protein analysis, we compared the proteomes from leaves of non-heading Chinese cabbage seedlings that were infected with H. parasitica or that were only treated with water at different time points post-infection. By MS analysis, 91 protein spots with significant differences in abundance (>2-fold, p<0.05) were identified in mock- and H. parasitica-inoculated leaves. Next, a resistance strategy for incompatible interactions was proposed. This network consisted of several functional components, including enhanced ethylene biosynthesis and energy supply, balanced ROS production and scavenging, accelerated protein metabolism and photorespiratory, reduced photosynthesis, and induced photosystem repair. These findings increase our knowledge of incompatible interactions between plants and pathogens and also provide new insight regarding the function of plant molecular processes, which should assist in the discovery of new strategies for pathogen control.

BIOLOGICAL SIGNIFICANCE

This study reported the proteomic analysis of the incompatible interactions between non-heading Chinese cabbage and downy mildew using 2-DE and MS. In total, 91 protein spots that were related to the resistance response were identified. These proteins were assigned to different functional categories, such as amino acid and carbohydrate metabolism, photosynthesis and photorespiration, protein metabolism, signal transduction, redox homeostasis, and ethylene biosynthesis. Meanwhile, several key proteins were determined to be associated with ethylene signalling, ROS scavenging and resistance-related proteins. Consistent with these results, the expression of ethylene biosynthesis genes and response genes, as well as the activity of antioxidant enzymes, increased after inoculation. These findings provide new insight for further understanding the molecular mechanisms of plant resistance.

Dark-adapted spinach thylakoid protein heterogeneity offers insights into the photosystem II repair cycle

In higher plants, thylakoid membrane protein complexes show lateral heterogeneity in their distribution: photosystem (PS) II complexes are mostly located in grana stacks, whereas PSI and adenosine triphosphate (ATP) synthase are mostly found in the stroma-exposed thylakoids. However, recent research has revealed strong dynamics in distribution of photosystems and their light harvesting antenna along the thylakoid membrane. Here, the dark-adapted spinach (Spinacia oleracea L.) thylakoid network was mechanically fragmented and the composition of distinct PSII-related proteins in various thylakoid subdomains was analyzed in order to get more insights into the composition and localization of various PSII subcomplexes and auxiliary proteins during the PSII repair cycle. Most of the PSII subunits followed rather equal distribution with roughly 70% of the proteins located collectively in the grana thylakoids and grana margins; however, the low molecular mass subunits PsbW and PsbX as well as the PsbS proteins were found to be more exclusively located in grana thylakoids. The auxiliary proteins assisting in repair cycle of PSII were mostly located in stroma-exposed thylakoids, with the exception of THYLAKOID LUMEN PROTEIN OF 18.3 (TLP18.3), which was more evenly distributed between the grana and stroma thylakoids. The TL29 protein was present exclusively in grana thylakoids. Intriguingly, PROTON GRADIENT REGULATION5 (PGR5) was found to be distributed quite evenly between grana and stroma thylakoids, whereas PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE1 (PGRL1) was highly enriched in the stroma thylakoids and practically missing from the grana cores. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy.

Understanding the roles of the thylakoid lumen in photosynthesis regulation

It has been known for a long time that the thylakoid lumen provides the environment for oxygen evolution, plastocyanin-mediated electron transfer, and photoprotection. More recently lumenal proteins have been revealed to play roles in numerous processes, most often linked with regulating thylakoid biogenesis and the activity and turnover of photosynthetic protein complexes, especially the photosystem II and NAD(P)H dehydrogenase-like complexes. Still, the functions of the majority of lumenal proteins in Arabidopsis thaliana are unknown. Interestingly, while the thylakoid lumen proteome of at least 80 proteins contains several large protein families, individual members of many protein families have highly divergent roles. This is indicative of evolutionary pressure leading to neofunctionalization of lumenal proteins, emphasizing the important role of the thylakoid lumen for photosynthetic electron transfer and ultimately for plant fitness. Furthermore, the involvement of anterograde and retrograde signaling networks that regulate the expression and activity of lumen proteins is increasingly pertinent. Recent studies have also highlighted the importance of thiol/disulfide modulation in controlling the functions of many lumenal proteins and photosynthetic regulation pathways.

The GreenCut: re-evaluation of physiological role of previously studied proteins and potential novel protein functions

Based on comparative genomics, a list of proteins present in the green algal, flowering and nonflowering plant lineages, but not detected in nonphotosynthetic organisms, was assembled (Merchant et al., Science 318:245-250, 2007; Karpowicz et al., J Biol Chem 286:21427-21439, 2011). This protein grouping, previously designated the GreenCut, was established using stringent comparative genomic criteria; they are those Chlamydomonas reinhardtii proteins with orthologs in Arabidopsis thaliana, Physcomitrella patens, Oryza sativa, Populus tricocarpa and at least one of the three Ostreococcus species with fully sequenced genomes, but not in bacteria, yeast, fungi or mammals. Many GreenCut proteins are also present in red algae and diatoms and a subset of 189 have been identified as encoded on nearly all cyanobacterial genomes. Of the current GreenCut proteins (597 in total), approximately half have been studied previously. The functions or activities of a number of these proteins have been deduced from phenotypic analyses of mutants (defective for genes encoding specific GreenCut proteins) of A. thaliana, and in many cases the assigned functions do not exist in C. reinhardtii. Therefore, precise physiological functions of several previously studied GreenCut proteins are still not clear. The GreenCut also contains a number of proteins with certain conserved domains. Three of the most highly conserved domains are the FK506 binding, cyclophilin and PAP fibrillin domains; most members of these gene families are not well characterized. In general, our analysis of the GreenCut indicates that many processes critical to green lineage organisms remain unstudied or poorly characterized. We have begun to examine the functions of some GreenCut proteins in detail. For example, our work on the CPLD38 protein has demonstrated that it has an essential role in photosynthetic function and the stability of the cytochrome b 6 f complex.

In-depth proteome analysis of the rubber particle of Hevea brasiliensis (para rubber tree)

The rubber particle is a special organelle in which natural rubber is synthesised and stored in the laticifers of Hevea brasiliensis. To better understand the biological functions of rubber particles and to identify the candidate rubber biosynthesis-related proteins, a comprehensive proteome analysis was performed on H. brasiliensis rubber particles using shotgun tandem mass spectrometry profiling approaches-resulting in a thorough report on the rubber particle proteins. A total of 186 rubber particle proteins were identified, with a range in relative molecular mass of 3.9-194.2 kDa and in isoelectric point values of 4.0-11.2. The rubber particle proteins were analysed for gene ontology and could be categorised into eight major groups according to their functions: including rubber biosynthesis, stress- or defence-related responses, protein processing and folding, signal transduction and cellular transport. In addition to well-known rubber biosynthesis-related proteins such as rubber elongation factor (REF), small rubber particle protein (SRPP) and cis-prenyl transferase (CPT), many proteins were firstly identified to be on the rubber particles, including cyclophilin, phospholipase D, cytochrome P450, small GTP-binding protein, clathrin, eukaryotic translation initiation factor, annexin, ABC transporter, translationally controlled tumour protein, ubiquitin-conjugating enzymes, and several homologues of REF, SRPP and CPT. A procedure of multiple reaction monitoring was established for further protein validation. This comprehensive proteome data of rubber particles would facilitate investigation into molecular mechanisms of biogenesis, self-homeostasis and rubber biosynthesis of the rubber particle, and might serve as valuable biomarkers in molecular breeding studies of H. brasiliensis and other alternative rubber-producing species.

Regulatory factors for the assembly of thylakoid membrane protein complexes

Major multi-protein photosynthetic complexes, located in thylakoid membranes, are responsible for the capture of light and its conversion into chemical energy in oxygenic photosynthetic organisms. Although the structures and functions of these photosynthetic complexes have been explored, the molecular mechanisms underlying their assembly remain elusive. In this review, we summarize current knowledge of the regulatory components involved in the assembly of thylakoid membrane protein complexes in photosynthetic organisms. Many of the known regulatory factors are conserved between prokaryotes and eukaryotes, whereas others appear to be newly evolved or to have expanded predominantly in eukaryotes. Their specific features and fundamental differences in cyanobacteria, green algae and land plants are discussed.

A Rice Immunophilin Gene, OsFKBP16-3, Confers Tolerance to Environmental Stress in Arabidopsis and Rice

The putative thylakoid lumen immunophilin, FKBP16-3, has not yet been characterized, although this protein is known to be regulated by thioredoxin and possesses a well-conserved CxxxC motif in photosynthetic organisms. Here, we characterized rice OsFKBP16-3 and examined the role of this gene in the regulation of abiotic stress in plants. FKBP16-3s are well conserved in eukaryotic photosynthetic organisms, including the presence of a unique disulfide-forming CxxxC motif in their N-terminal regions. OsFKBP16-3 was mainly expressed in rice leaf tissues and was upregulated by various abiotic stresses, including salt, drought, high light, hydrogen peroxide, heat and methyl viologen. The chloroplast localization of OsFKBP16-3-GFP was confirmed through the transient expression of OsFKBP16-3 in Nicotiana benthamiana leaves. Transgenic Arabidopsis and transgenic rice plants that constitutively expressed OsFKBP16-3 exhibited increased tolerance to salinity, drought and oxidative stresses, but showed no change in growth or phenotype, compared with vector control plants, when grown under non-stressed conditions. This is the first report to demonstrate the potential role of FKBP16-3 in the environmental stress response, which may be regulated by a redox relay process in the thylakoid lumen, suggesting that artificial regulation of FKBP16-3 expression is a candidate for stress-tolerant crop breeding.

Photosystem II assembly: from cyanobacteria to plants

Photosystem II (PSII) is an integral-membrane, multisubunit complex that initiates electron flow in oxygenic photosynthesis. The biogenesis of this complex machine involves the concerted assembly of at least 20 different polypeptides as well as the incorporation of a variety of inorganic and organic cofactors. Many factors have recently been identified that constitute an integrative network mediating the stepwise assembly of PSII components. One recurring theme is the subcellular organization of the assembly process in specialized membranes that form distinct biogenesis centers. Here, we review our current knowledge of the molecular components and events involved in PSII assembly and their high degree of evolutionary conservation.