Identification of a novel protein, CRR7, required for the stabilization of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis

Comparative Analysis of Chloroplast Genomes within Saxifraga (Saxifragaceae) Takes Insights into Their Genomic Evolution and Adaption to the High-Elevation Environment

Saxifraga species are widely distributed in alpine and arctic regions in the Northern hemisphere. Highly morphological diversity within this genus brings great difficulties for species identification, and their typical highland living properties make it interesting how they adapt to the extreme environment. Here, we newly generated the chloroplast (cp) genomes of two Saxifraga species and compared them with another five Saxifraga cp genomes to understand the characteristics of cp genomes and their potential roles in highland adaptation. The genome size, structure, gene content, GC content, and codon usage pattern were found to be highly similar. Cp genomes ranged from 146,549 bp to 151,066 bp in length, most of which comprised 130 predicted genes. Yet, due to the expansion of IR regions, the second copy of rps19 in Saxifraga stolonifera was uniquely kept. Through sequence divergence analysis, we identified seven hypervariable regions and detected some signatures of regularity associated with genetic distance. We also identified 52 to 89 SSRs and some long repeats among seven Saxifraga species. Both ML and BI phylogenetic analyses confirmed that seven Saxifraga species formed a monophyletic clade in the Saxifragaceae family, and their intragenus relationship was also well supported. Additionally, the ndhI and ycf1 genes were considered under positive selection in species inhabiting relatively high altitudes. Given the conditions of intense light and low CO₂ concentration in the highland, the products of these two genes might participate in the adaptation to the extreme environment.

Genome-wide association identifies a missing hydrolase for tocopherol synthesis in plants

SignificanceTocopherols (vitamin E) are plant-synthesized, lipid-soluble antioxidants whose dietary intake, primarily from seed oils, is essential for human health. Tocopherols contain a phytol-derived hydrophobic tail whose in vivo source has been elusive. The most significant genome-wide association signal for Arabidopsis seed tocopherols identified an uncharacterized, seed-specific esterase (VTE7) localized to the chloroplast envelope, where tocopherol synthesis occurs. VTE7 disruption and overexpression had large impacts on tissue tocopherol contents with metabolic phenotypes consistent with release of prenyl alcohols, including phytol, during chlorophyll synthesis, rather than from the bulk degradation of thylakoid chlorophylls as has long been assumed. Understanding the source of phytol for tocopherols will enable breeding and engineering plants for vitamin E biofortification and enhanced stress resilience.

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.

The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I

In natural habitats, plants have developed sophisticated regulatory mechanisms to optimize the photosynthetic electron transfer rate at the maximum efficiency and cope with the changing environments. Maintaining proper P700 oxidation at photosystem I (PSI) is the common denominator for most regulatory processes of photosynthetic electron transfers. However, the molecular complexes and cofactors involved in these processes and their function(s) have not been fully clarified. Here, we identified a redox-active chloroplast protein, the triplet-cysteine repeat protein (TCR). TCR shared similar expression profiles with known photosynthetic regulators and contained two triplet-cysteine motifs (CxxxCxxxC). Biochemical analysis indicated that TCR localizes in chloroplasts and has a [3Fe-4S] cluster. Loss of TCR limited the electron sink downstream of PSI during dark-to-light transition. Arabidopsis pgr5-tcr double mutant reduced growth significantly and showed unusual oxidation and reduction of plastoquinone pool. These results indicated that TCR is involved in electron flow(s) downstream of PSI, contributing to P700 oxidation.

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P700 oxidation at photosystem I is important for regulation of photosynthesis

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TCR is a redox active chloroplast protein harboring a 3Fe-4S iron-sulfur cluster

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TCR controls electron flow around photosystem I, contributing to P700 oxidation

Genome-wide Association Study Reveals that the Aquaporin NIP1;1 Contributes to Variation in Hydrogen Peroxide Sensitivity in Arabidopsis thaliana

Hydrogen peroxide (H₂O₂) is a reactive oxygen species that affects cell signaling in various plant defense responses and induces programmed cell death. To identify the new components associated with H₂O₂ signaling and tolerance, we conducted a genome-wide association study (GWAS) on the root growth of 133 Arabidopsis thaliana accessions grown in the presence of toxic H₂O₂ levels. The most significant SNPs were associated with a cluster of chromosome 4 genes encoding an aquaporin NODULIN 26-LIKE INTRINSIC PROTEIN 1; 1 (NIP1;1), an NB-ARC domain-containing disease resistance protein (AT4G19050), and a putative membrane lipoprotein (AT4G19070). The expression level of NIP1;1 was relatively high in A. thaliana accessions sensitive to H₂O₂. Additionally, overexpression of NIP1;1 in a tolerant accession (e.g., Col-0) increased the sensitivity of transgenic plants to H₂O₂. An in planta β-glucuronidase reporter assay revealed that variations in the NIP1;1 promoter were responsible for the differences of its expression level in H₂O₂-tolerant and -sensitive accessions. Cell death was extensive and H₂O₂ levels were high in the roots of H₂O₂-sensitive and NIP1;1-overexpressing accessions. Together, our results indicate that the aquaporin NIP1;1 is a key determinant of the sensitivity of A. thaliana to H₂O₂, and contributes to the phenotypic variations detected by our GWAS.

Increasing cyclic electron flow is related to Na+ sequestration into vacuoles for salt tolerance in soybean

In land plants, the NAD(P)H dehydrogenase (NDH) complex reduces plastoquinones and drives cyclic electron flow (CEF) around PSI. It also produces extra ATP for photosynthesis and improves plant fitness under conditions of abiotic environmental stress. To elucidate the role of CEF in salt tolerance of the photosynthetic apparatus, Na(+) concentration, chlorophyll fluorescence, and expression of NDH B and H subunits, as well as of genes related to cellular and vacuolar Na(+) transport, were monitored. The salt-tolerant Glycine max (soybean) variety S111-9 exhibited much higher CEF activity and ATP accumulation in light than did the salt-sensitive variety Melrose, but similar leaf Na(+) concentrations under salt stress. In S111-9 plants, ndhB and ndhH were highly up-regulated under salt stress and their corresponding proteins were maintained at high levels or increased significantly. Under salt stress, S111-9 plants accumulated Na(+) in the vacuole, but Melrose plants accumulated Na(+) in the chloroplast. Compared with Melrose, S111-9 plants also showed higher expression of some genes associated with Na(+) transport into the vacuole and/or cell, such as genes encoding components of the CBL10 (calcineurin B-like protein 10)-CIPK24 (CBL-interacting protein kinase 24)-NHX (Na(+)/H(+) antiporter) and CBL4 (calcineurin B-like protein 4)-CIPK24-SOS1 (salt overly sensitive 1) complexes. Based on the findings, it is proposed that enhanced NDH-dependent CEF supplies extra ATP used to sequester Na(+) in the vacuole. This reveals an important mechanism for salt tolerance in soybean and provides new insights into plant resistance to salt stress.

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.

Identification of a cyanobacterial CRR6 protein, Slr1097, required for efficient assembly of NDH-1 complexes in Synechocystis sp. PCC 6803

Despite significant progress in clarifying the subunit compositions and functions of the multiple NADPH dehydrogenase (NDH-1) complexes in cyanobacteria, the subunit maturation and assembly of their NDH-1 complexes are poorly understood. By transformation of wild-type cells with a transposon-tagged library, we isolated three mutants of Synechocystis sp. PCC 6803 defective in NDH-1-mediated cyclic electron transfer and unable to grow under high light conditions. All the mutants were tagged in the same slr1097 gene, encoding an unknown protein that shares significant homology with the Arabidopsis protein chlororespiratory reduction 6 (CRR6). The slr1097 product was localized in the cytoplasm and was required for efficient assembly of NDH-1 complexes. Analysis of the interaction of Slr1097 with 18 subunits of NDH-1 complexes using a yeast two-hybrid system indicated a strong interaction with NdhI but not with other Ndh subunits. Absence of Slr1097 resulted in a significant decrease of NdhI in the cytoplasm, but not of other Ndh subunits including NdhH, NdhK and NdhM; the decrease was more evident in the cytoplasm than in the thylakoid membranes. In the ∆slr1097 mutant, NdhH, NdhI, NdhK and NdhM were hardly detectable in the NDH-1M complex, whereas almost half the wild-type levels of these subunits were present in NDH-1L complex; similar results were observed in the NdhI-less mutant. These results suggest that Slr1097 is involved in the maturation of NdhI, and that assembly of the NDH-1M complex is strongly dependent on this factor. Maturation of NdhI appears not to be crucial to assembly of the NDH-1L complex.

Thioredoxin m4 controls photosynthetic alternative electron pathways in Arabidopsis

In addition to the linear electron flow, a cyclic electron flow (CEF) around photosystem I occurs in chloroplasts. In CEF, electrons flow back from the donor site of photosystem I to the plastoquinone pool via two main routes: one that involves the Proton Gradient Regulation5 (PGR5)/PGRL1 complex (PGR) and one that is dependent of the NADH dehydrogenase-like complex. While the importance of CEF in photosynthesis and photoprotection has been clearly established, little is known about its regulation. We worked on the assumption of a redox regulation and surveyed the putative role of chloroplastic thioredoxins (TRX). Using Arabidopsis (Arabidopsis thaliana) mutants lacking different TRX isoforms, we demonstrated in vivo that TRXm4 specifically plays a role in the down-regulation of the NADH dehydrogenase-like complex-dependent plastoquinone reduction pathway. This result was confirmed in tobacco (Nicotiana tabacum) plants overexpressing the TRXm4 orthologous gene. In vitro assays performed with isolated chloroplasts and purified TRXm4 indicated that TRXm4 negatively controls the PGR pathway as well. The physiological significance of this regulation was investigated under steady-state photosynthesis and in the pgr5 mutant background. Lack of TRXm4 reversed the growth phenotype of the pgr5 mutant, but it did not compensate for the impaired photosynthesis and photoinhibition sensitivity. This suggests that the physiological role of TRXm4 occurs in vivo via a mechanism distinct from direct up-regulation of CEF.

Solution NMR structure of Asl3597 from Nostoc sp. PCC7120, the first structure from protein domain family PF12095, reveals a novel fold

The protein domain family PF12095 (DUF3571) is a functionally uncharacterized family of small proteins conserved from cyanobacteria to plants that are typically 85 to 95 amino acids in length in cyanobacteria. In this report, we describe the solution NMR structure of the 86-residue protein Asl3597 from Nostoc sp. PCC7120. The structure of Asl3597, which constitutes the first three-dimensional structure from protein family PF12095, has a unique α/β sandwich fold consisting of four anti-parallel β-strands opposite three continuous α-helices. Asl3597 may have a role in the assembly of the hydrophilic subcomplex of the cyanobacterial NAD(P)H complex as suggested by data for the orthologous Chlororespiratory reduction 7 protein from Arabidopsis thaliana.

The pentatricopeptide repeat protein OTP87 is essential for RNA editing of nad7 and atp1 transcripts in Arabidopsis mitochondria

In plant organelles, RNA editing is a post-transcriptional mechanism that converts specific cytidines to uridines in RNA of both mitochondria and plastids, altering the information encoded by the gene. The cytidine to be edited is determined by a cis-element surrounding the editing site that is specifically recognized and bound by a trans-acting factor. All the trans-acting editing factors identified so far in plant organelles are members of a large protein family, the pentatricopeptide repeat (PPR) proteins. We have identified the Organelle Transcript Processing 87 (OTP87) gene, which is required for RNA editing of the nad7-C24 and atp1-C1178 sites in Arabidopsis mitochondria. OTP87 encodes an E-subclass PPR protein with an unusually short E-domain. The recombinant protein expressed in Escherichia coli specifically binds to RNAs comprising 30 nucleotides upstream and 10 nucleotides downstream of the nad7-C24 and atp1-C1178 editing sites. The loss-of-function of OTP87 results in small plants with growth and developmental delays. In the otp87 mutant, the amount of assembled respiratory complex V (ATP synthase) is highly reduced compared with the wild type suggesting that the amino acid alteration in ATP1 caused by loss of editing at the atp1-C1178 site affects complex V assembly in mitochondria.

Update on chloroplast research: new tools, new topics, and new trends

Chloroplasts, the green differentiation form of plastids, are the sites of photosynthesis and other important plant functions. Genetic and genomic technologies have greatly boosted the rate of discovery and functional characterization of chloroplast proteins during the past decade. Indeed, data obtained using high-throughput methodologies, in particular proteomics and transcriptomics, are now routinely used to assign functions to chloroplast proteins. Our knowledge of many chloroplast processes, notably photosynthesis and photorespiration, has reached such an advanced state that biotechnological approaches to crop improvement now seem feasible. Meanwhile, efforts to identify the entire complement of chloroplast proteins and their interactions are progressing rapidly, making the organelle a prime target for systems biology research in plants.

Structure and biogenesis of the chloroplast NAD(P)H dehydrogenase complex

Eleven genes (ndhA-ndhK) encoding proteins homologous to the subunits of bacterial and mitochondrial NADH dehydrogenase (complex I) were found in the plastid genome of most land plants. These genes encode subunits of the chloroplast NAD(P)H dehydrogenase (NDH) complex involved in photosystem I (PSI) cyclic electron transport and chlororespiration. Although the chloroplast NDH is believed to be closely and functionally related to the cyanobacterial NDH-1L complex, extensive proteomic, genetic and bioinformatic studies have discovered many novel subunits that are specific to higher plants. On the basis of extensive mutant characterization, the chloroplast NDH complex is divided into four parts, the A, B, membrane and lumen subcomplexes, of which subunits in the B and lumen subcomplexes are specific to higher plants. These results suggest that the structure of NDH has been drastically altered during the evolution of land plants. Furthermore, chloroplast NDH interacts with multiple copies of PSI to form the unique NDH-PSI supercomplex. Two minor light-harvesting-complex I (LHCI) proteins, Lhca5 and Lhca6, are required for the specific interaction between NDH and PSI. The evolution of chloroplast NDH in land plants may be required for development of the function of NDH to alleviate oxidative stress in chloroplasts. In this review, we summarize recent progress on the subunit composition and structure of the chloroplast NDH complex, as well as the information on some factors involved in its assembly. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.

Chloroplast stromal proteins, CRR6 and CRR7, are required for assembly of the NAD(P)H dehydrogenase subcomplex A in Arabidopsis

In higher plants, the chloroplast NAD(P)H dehydrogenase (NDH) complex mediates chlororespiration and photosystem I (PSI) cyclic electron transport in thylakoid membranes. Because of its low abundance and fragility, our knowledge on the assembly of chloroplast NDH is very limited, and some nuclear-encoded factors may be involved in this process. We show here that two Arabidopsis proteins, CHLORORESPIRATORY REDUCTION 6 (CRR6) and CRR7, which were previously identified in mutants specifically defective in NDH accumulation, are present in the stroma, and their stability is independent of the NDH complex, suggesting that they are unlikely to be NDH subunits. Blue native PAGE analysis showed that the accumulation of NDH subcomplex A, which is a core part of NDH that is conserved in divergent species, was specifically impaired in the crr6 and crr7-1 mutants. However, the expression of plastid-encoded genes encoding the subcomplex A subunits was not affected, suggesting that CRR6 and CRR7 are involved in post-translational steps during the biogenesis of subcomplex A. We also discovered that a substantial quantity of NdhH is present in several protein complexes in the chloroplast stroma, possibly as early assembly intermediates of subcomplex A. Although the accumulation of these stromal complexes was not affected in crr6 or crr7-1, CRR6 was co-purified with NdhH, implying that CRR6 functions in the later step of subcomplex-A biogenesis. Accumulation of CRR7 was independent of that of CRR6; we propose that CRR7 functions in a different step in subcomplex-A biogenesis from CRR6.

Three PsbQ-like proteins are required for the function of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis

Arabidopsis has three PsbQ-like (PQL) proteins in addition to the PsbQ subunit of the oxygen-evolving complex of PSII. Recent bioinformatic and proteomic studies suggested that the two PQL proteins, PQL1 (At1g14150) and PQL2 (At3g01440), might function in the chloroplast NAD(P)H dehydrogenase (NDH) complex; however, their molecular function has not been characterized. In this study, we examined the function of the chloroplast NDH in the Arabidopsis pql1 and pql2 mutants. Post-illumination increases in Chl fluorescence, which are caused by an NDH-dependent cyclic electron flow, were absent in both mutants, indicating that PQL1 and PQL2 are required for NDH activity. In the thylakoid membranes of wild-type plants, PQL1 and PQL2 were tightly associated with the NDH-PSI supercomplex and protected from protease treatments, while unassembled PQLs were not stably accumulated in mutants lacking known NDH subunits. Subunit stability of the NDH complex was affected differently in the thylakoid membranes of the pql1 and pql2 mutants. These data indicate that PQL1 and PQL2 are novel NDH subunits and differ in their functional roles and in their binding sites in the NDH complex. Furthermore, functional analysis on PQL3 (At2g01918) using the pql3 mutant suggests that PQL3 is also required for NDH activity. Proteins homologous to each PQL protein are found in various plant species, but not in cyanobacteria, algae, mosses or ferns. These results suggest that seed plants that have NDH activity in chloroplasts specifically developed three PQL proteins for the function of the chloroplast NDH complex.

A qualitative analysis of the regulation of cyclic electron flow around photosystem I from the post-illumination chlorophyll fluorescence transient in Arabidopsis: a new platform for the in vivo investigation of the chloroplast redox state

A transient in chlorophyll fluorescence after cessation of actinic light illumination, which has been ascribed to electron donation from stromal reductants to plastoquinone (PQ) by the NAD(P)H-dehydrogenase (NDH) complex, was investigated in Arabidopsis thaliana. The transient was absent in air in a mutant lacking the NDH complex (ndhM). However, in ndhM, the transient was detected in CO(2)-free air containing 2% O(2). To investigate the reason, ndhM was crossed with a pgr5 mutant impaired in ferredoxin (Fd)-dependent electron donation from NADPH to PQ, which is known to be redundant for NDH-dependent PQ reduction in the cyclic electron flow around photosystem I (PSI). In ndhM pgr5, the transient was absent even in CO(2)-free air with 2% O(2), demonstrating that the post-illumination transient can also be induced by the Fd- (or PGR5)-dependent PQ reduction. On the other hand, the transient increase in chlorophyll fluorescence was found to be enhanced in normal air in a mutant impaired in plastid fructose-1,6-bisphosphate aldolase (FBA) activity. The mutant, termed fba3-1, offers unique opportunities to examine the relative contribution of the two paths, i.e., the NDH- and Fd- (or PGR5)-dependent paths, on the PSI cyclic electron flow. Crossing fba3-1 with either ndhM or pgr5 and assessing the transient suggested that the main route for the PSI cyclic electron flow shifts from the NDH-dependent path to the Fd-dependent path in response to sink limitation of linear electron flow.

Towards characterization of the chloroplast NAD(P)H dehydrogenase complex

The NAD(P)H dehydrogenase (NDH) complex in chloroplast thylakoid membranes functions in cyclic electron transfer, and in chlororespiration. NDH is composed of at least 15 subunits, including both chloroplast- and nuclear-encoded proteins. During the past few years, extensive proteomic and genetic research on the higher plant NDH complex has been carried out, resulting in identification of several novel nuclear-encoded subunits. In addition, a number of auxiliary proteins, which mainly regulate the expression of chloroplast-encoded ndh genes as well as the assembly and stabilization of the NDH complex, have been discovered and characterized. In the absence of detailed crystallographic data, the structure of the NDH complex has remained obscure, and therefore the role of several NDH-associated nuclear-encoded proteins either as auxiliary proteins or structural subunits remains uncertain. In this review, we summarize the current knowledge on the subunit composition and assembly process of the chloroplast NDH complex. In addition, a novel oligomeric structure of NDH, the PSI/NDH supercomplex, is discussed.

Quantitative analysis of the relationship between induction kinetics of chlorophyll fluorescence and function of genes in the cyanobacterium Synechocystis sp. PCC 6803

We developed here the quantitative and objective method to analyze chlorophyll fluorescence from the cyanobacterium Synechocystis sp. PCC 6803 in the aim of systematic examination of gene function. The overall similarity of the chlorophyll fluorescence induction kinetics was evaluated for 499 mutants. Mutants of 333 genes showed the difference in the fluorescence kinetics from that of wild type, indicating the wide interaction of photosynthesis with other metabolisms. Hierarchical clustering of the similarity of the mutants enables us to group together the mutants having defect in the regulation of photosystem stoichiometry as well as those having defects in respiration or other functions. Furthermore, wild-type cells treated with inhibitors of respiration and mutants of genes involved in respiration shared similar induction kinetics. Apparently, quantitative comparison of the induction kinetics could be useful to analyze the function of genes as well as to predict the target sites of various chemicals.

A novel nuclear-encoded protein, NDH-dependent cyclic electron flow 5, is essential for the accumulation of chloroplast NAD(P)H dehydrogenase complexes

The chloroplast NAD(P)H dehydrogenase (NDH) complex, which reduces plastoquinones in thylakoid membranes, is involved in PSI cyclic electron flow and chlororespiration. In addition to land plants, the NDH complex is conserved in cyanobacteria. In this study, we identified a novel NDH-related gene of Arabidopsis, NDH-dependent cyclic electron flow 5 (NDF5, At1g55370). Post-illumination increases in chlorophyll fluorescence were absent in ndf5 mutant plants, which indicated that NDF5 is essential for NDH activity. Sequence analysis did not reveal any known functional motifs in NDF5, but there was some homology in amino acid sequence between NDF5 and NDF2, a known NDH subunit. NDF5 and NDF2 homologs were present in higher plants, but not cyanobacteria. A single homolog, which had similarity to both NDF5 and NDF2, was identified in the moss Physcomitrella patens. Immunoblot analysis showed that NDF5 localizes to membrane fractions of chloroplasts. The stability of NdhH, a subunit of the NDH complex, as well as NDF5 and NDF2, was decreased in ndf5, ndf2 and double ndf2/ndf5 mutants, resulting in a loss of NDH activity in these mutants. These results indicated that both NDF5 and NDF2 have essential functions in the stabilization of the NDH complex. We propose that NDF5 and NDF2 were acquired by land plants during evolution, and that in higher plants both NDF5 and NDF2 are critical to regulate NDH activity and each other's protein stability, as well as the stability of additional NDH subunits.

Cell-type-specific differentiation of chloroplasts in C4 plants

In leaves of C4 grasses such as maize, photosynthetic activities are partitioned between bundle-sheath and mesophyll cells, leading to increased photosynthetic yield, particularly under stress conditions. As we discuss here, recent comparative chloroplast proteome analyses in maize have shown specific adaptation to C4-cell-specific differentiation of the photosynthetic apparatus, primary and secondary metabolism and metabolite transporters, as well as the chloroplast protein homeostasis machinery. Furthermore, a novel bundle-sheath-enriched 1000-kDa NADPH dehydrogenase 'supercomplex' has been identified, and we discuss its possible role in inorganic carbon concentration. These breakthroughs provide new opportunities to further unravel C4 pathways and to increase crop productivity through metabolic engineering of C4 pathways into C3 plants, such as rice.

Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches

Chloroplastic NAD(P)H dehydrogenase (NDH) plays a role in cyclic electron flow around photosystem I to produce ATP, especially in adaptation to environmental changes. Although the NDH complex contains 11 subunits that are homologous to NADH:ubiquinone oxidoreductase (complex I; EC 1.6.5.3), recent genetic and biological studies have indicated that NDH also comprises unique subunits. We describe here an in silico approach based on co-expression analysis and phylogenetic profiling that was used to identify 65 genes as potential candidates for NDH subunits. Characterization of 21 Arabidopsis T-DNA insertion mutants among these ndh gene candidates indicated that three novel ndf (NDH-dependent cyclic electron flow) mutants (ndf1, ndf2 and ndf4) had impaired NDH activity as determined by measurement of chlorophyll fluorescence. The amount of NdhH subunit was greatly decreased in these mutants, suggesting that the loss of NDH activity was caused by a defect in accumulation of the NDH complex. In addition, NDF1, NDF2 and NDF4 proteins co-migrated with the NdhH subunit, as shown by blue native electrophoresis. These results strongly suggest that NDF proteins are novel subunits of the NDH complex. Further analysis revealed that the NDF1 and NDF2 proteins were unstable in the mutants lacking hydrophobic subunits of the NDH complex, but were stable in mutants lacking the hydrophilic subunits, suggesting that NDF1 and NDF2 interact with a hydrophobic sub-complex. NDF4 protein was predicted to possess a redox-active iron-sulfur cluster domain that may be involved in the electron transfer.

The chloroplast NAD(P)H dehydrogenase complex interacts with photosystem I in Arabidopsis

The chloroplast NAD(P)H dehydrogenase (NDH) complex is involved in photosystem I (PSI) cyclic and chlororespiratory electron transport in higher plants. Although biochemical and genetic evidence for its subunit composition has accumulated, it is not enough to explain the complexes putative activity of NAD(P)H-dependent plastoquinone reduction. We analyzed the NDH complex by using blue native PAGE and found that it interacts with PSI to form a novel supercomplex. Mutants lacking NdhL and NdhM accumulated a pigment-protein complex with a slightly lower molecular mass than that of the NDH-PSI supercomplex; this may be an intermediate supercomplex including PSI. This intermediate is unstable in mutants lacking NdhB, NdhD, or NdhF, implying that it includes some NDH subunits. Analysis of thylakoid membrane complexes using sucrose density gradient centrifugation supported the presence of the NDH-PSI supercomplex in vivo. Although the NDH complex exists as a monomer in etioplasts, it interacts with PSI to form a supercomplex within 48 h during chloroplast development.

Effect of PGR5 impairment on photosynthesis and growth in Arabidopsis thaliana

PGR5 has been reported as an important factor for the activity of the ferredoxin-dependent cyclic electron transport around PSI. To elucidate the role of PGR5 in C(3) photosynthesis, we characterized the photosynthetic electron transport rate (ETR), CO(2) assimilation and growth in the Arabidopsis thaliana pgr5 mutant at various irradiances and with CO(2) regimes. In low-light-grown pgr5, the CO(2) assimilation rate and ETR were similar to the those of the wild type at low irradiance, but decreased at saturating irradiance under photorespiratory conditions as well as non-photorespiratory conditions. Although non-photochemical quenching of chlorophyll fluorescence (NPQ) was not induced in the pgr5 mutant under steady-state photosynthesis, we show that it was induced under dark to light transition at low CO(2) concentration. Under low light conditions in air, pgr5 showed the same growth as the wild type, but a significant growth reduction compared with the wild type at >150 mumol photons m(-2) s(-1). This growth impairment was largely suppressed under high CO(2) concentrations. Based on the intercellular CO(2) concentration dependency of CO(2) assimilation, ETR and P700 oxidation measurements, we conclude that reduction of photosynthesis and growth result from (i) ATP deficiency and (ii) inactivation of PSI. We discuss these data in relation to the role of PGR5-dependent regulatory mechanisms in tuning the ATP/NADPH ratio and preventing inactivation of PSI, especially under conditions of high irradiance or enhanced photorespiration.

Electron transport activities of Arabidopsis thaliana mutants with impaired chloroplastic NAD(P)H dehydrogenase

The activities of electron transport are compared between wild-type Arabidopsis and two Arabidopsis mutants deficient for the chloroplastic NAD(P)H dehydrogenase (NDH) which catalyzes cyclic electron transport around photosystem I. The quantum yield of photosystem II and the degree of non-photochemical quenching of chlorophyll fluorescence were of similar levels in the two NDH-deficient mutants and the wild type under non-stressed standard growth conditions. Stromal over-reduction was induced in Arabidopsis NDH mutants with high light treatment, as is the case in tobacco NDH mutants. However, unlike tobacco mutants, photoinhibition was not observed in the Arabidopsis NDH mutants.

NDF6: a thylakoid protein specific to terrestrial plants is essential for activity of chloroplastic NAD(P)H dehydrogenase in Arabidopsis

NAD(P)H dehydrogenase (NDH) is a homolog of respiratory complex I and mediates one of the two pathways of cyclic electron flow around PSI (CEF I). Although 15 ndh subunits have been identified in the chloroplastic and nuclear genomes of higher plants, no electron accepter subunits have been identified to date. To identify the missing chloroplastic NDH subunits, we undertook an in silico approach based on co-expression analysis. In this report, we characterized the novel gene NDF6 (NDH-dependent flow 6; At1g18730) which encodes a protein that is essential for NDH activity. NDF6 has one transmembrane domain and is localized in the thylakoid membrane fraction. Homologous proteins of NDF6 were identified in the genomes of terrestrial plants; however, no homologs have been found in cyanobacteria, which are thought to be the origin of chloroplasts and have a minimal NDH complex unit. NDF6 is unstable in ndhB-impaired or disrupted mutants of higher plants in which the chloroplastic NDH complex is thought to be degraded. These results suggest that NDF6 is a novel subunit of chloroplastic NDH that was added to terrestrial plants during evolution.

Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells

Chloroplasts of maize leaves differentiate into specific bundle sheath (BS) and mesophyll (M) types to accommodate C(4) photosynthesis. Chloroplasts contain thylakoid and envelope membranes that contain the photosynthetic machineries and transporters but also proteins involved in e.g. protein homeostasis. These chloroplast membranes must be specialized within each cell type to accommodate C(4) photosynthesis and regulate metabolic fluxes and activities. This quantitative study determined the differentiated state of BS and M chloroplast thylakoid and envelope membrane proteomes and their oligomeric states using innovative gel-based and mass spectrometry-based protein quantifications. This included native gels, iTRAQ, and label-free quantification using an LTQ-Orbitrap. Subunits of Photosystems I and II, the cytochrome b(6)f, and ATP synthase complexes showed average BS/M accumulation ratios of 1.6, 0.45, 1.0, and 1.33, respectively, whereas ratios for the light-harvesting complex I and II families were 1.72 and 0.68, respectively. A 1000-kDa BS-specific NAD(P)H dehydrogenase complex with associated proteins of unknown function containing more than 15 proteins was observed; we speculate that this novel complex possibly functions in inorganic carbon concentration when carboxylation rates by ribulose-bisphosphate carboxylase/oxygenase are lower than decarboxylation rates by malic enzyme. Differential accumulation of thylakoid proteases (Egy and DegP), state transition kinases (STN7,8), and Photosystem I and II assembly factors was observed, suggesting that cell-specific photosynthetic electron transport depends on post-translational regulatory mechanisms. BS/M ratios for inner envelope transporters phosphoenolpyruvate/P(i) translocator, Dit1, Dit2, and Mex1 were determined and reflect metabolic fluxes in carbon metabolism. A wide variety of hundreds of other proteins showed differential BS/M accumulation. Mass spectral information and functional annotations are available through the Plant Proteome Database. These data are integrated with previous data, resulting in a model for C(4) photosynthesis, thereby providing new rationales for metabolic engineering of C(4) pathways and targeted analysis of genetic networks that coordinate C(4) differentiation.

Distinct functions for the two PsbP-like proteins PPL1 and PPL2 in the chloroplast thylakoid lumen of Arabidopsis

PsbP, an extrinsic subunit of photosystem II (PSII), is a nuclear-encoded protein that optimizes the water-splitting reaction in vivo. In addition to PsbP, higher plants have two nuclear-encoded genes for PsbP homologs (PsbP-like proteins [PPLs]) that show significant sequence similarity to a cyanobacterial PsbP homolog (cyanoP); however, the function of PPLs in higher plants has not yet been elucidated. In this study, we characterized Arabidopsis (Arabidopsis thaliana) mutants lacking either of two PPLs, PPL1 and PPL2. Phylogenetic analysis suggests that PPL1 would be an ortholog of cyanoP, and PPL2 and PsbP may have a paralogous relationship with PPL1. Analysis on mRNA expression profiles showed that PPL1 expressed under stress conditions and PPL2 coexpressed with the subunits of chloroplast NAD(P)H dehydrogenase (NDH) complex. Consistent with these suggestions, PSII activity in a ppl1 mutant was more sensitive to high-intensity light than wild type, and the recovery of photoinhibited PSII activity was delayed in ppl1 plants. Therefore, PPL1 is required for efficient repair of photodamaged PSII. Furthermore, the stoichiometric level and activity of the chloroplast NDH complex in thylakoids were severely decreased in a ppl2 mutant, demonstrating that PPL2 is a novel thylakoid lumenal factor required for accumulation of the chloroplast NDH complex. These results suggest that during endosymbiosis and subsequent gene transfer to the host nucleus, cyanoP from ancient cyanobacteria evolved into PPL1, PPL2, and PsbP, and each of them has a distinct role in photosynthetic electron transfer in Arabidopsis.

Dihydrodipicolinate reductase-like protein, CRR1, is essential for chloroplast NAD(P)H dehydrogenase in Arabidopsis

Chloroplast NAD(P)H dehydrogenase (NDH) is a homolog of the bacterial NADH dehydrogenase NDH-1 and is involved in cyclic electron transport around photosystem I. In higher plants, 14 subunits of the NDH complex have been identified. The subunit that contains the electron donor-binding site or an electron donor to NDH has not been determined. Arabidopsis crr1 (chlororespiratory reduction 1) mutants were isolated by chlorophyll fluorescence imaging on the basis of their lack of NDH activity. CRR1 is homologous to dihydrodipicolinate reductase (DHPR), which functions in a lysine biosynthesis pathway. However, the dihydrodipicolinate-binding motif was not conserved in CRR1, and the crr1 defect was specific to accumulation of the NDH complex, implying that CRR1 is not involved in lysine biosynthesis in Arabidopsis. Similarly to other nuclear-encoded genes for NDH subunits, CRR1 was expressed only in photosynthetic tissue. CRR1 contained a NAD(P)H-binding motif and was a candidate electron donor-binding subunit of the NDH complex. However, CRR1 was detected in the stroma but not in the thylakoid membranes, where the NDH complex is localized. Furthermore, CRR1 was stable in crr2-2 lacking the NDH complex. These results suggest that CRR1 is involved in biogenesis or stabilization of the NDH complex, possibly via the reduction of an unknown substrate.

Chlororespiration and cyclic electron flow around PSI during photosynthesis and plant stress response

Besides major photosynthetic complexes of oxygenic photosynthesis, new electron carriers have been identified in thylakoid membranes of higher plant chloroplasts. These minor components, located in the stroma lamellae, include a plastidial NAD(P)H dehydrogenase (NDH) complex and a plastid terminal plastoquinone oxidase (PTOX). The NDH complex, by reducing plastoquinones (PQs), participates in one of the two electron transfer pathways operating around photosystem I (PSI), the other likely involving a still uncharacterized ferredoxin-plastoquinone reductase (FQR) and the newly discovered PGR5. The existence of a complex network of mechanisms regulating expression and activity of the NDH complex, and the presence of higher amounts of NDH complex and PTOX in response to environmental stress conditions the phenotype of mutants, indicate that these components likely play a role in the acclimation of photosynthesis to changing environmental conditions. Based on recently published data, we propose that the NDH-dependent cyclic pathway around PSI participates to the ATP supply in conditions of high ATP demand (such as high temperature or water limitation) and together with PTOX regulates cyclic electron transfer activity by tuning the redox state of intersystem electron carriers. In response to severe stress conditions, PTOX associated to the NDH and/or the PGR5 pathway may also limit electron pressure on PSI acceptor and prevent PSI photoinhibition.

A novel nucleus-encoded chloroplast protein, PIFI, is involved in NAD(P)H dehydrogenase complex-mediated chlororespiratory electron transport in Arabidopsis

A transient rise in chlorophyll fluorescence after turning off actinic light reflects nonphotochemical reduction of the plastoquinone (PQ) pool. This process is dependent on the activity of the chloroplast NAD(P)H dehydrogenase (NDH) complex, which mediates electron flow from stromal reductants to the PQ pool. In this study, we characterized an Arabidopsis (Arabidopsis thaliana) T-DNA insertion mutant pifi (for postillumination chlorophyll fluorescence increase), which possesses an intact NDH complex, but lacks the NDH-dependent chlorophyll fluorescence increase after turning off actinic light. The nuclear gene PIFI (At3g15840) containing the T-DNA insertion encodes a chloroplast-targeted protein localized in the stroma and is annotated as a protein of unknown function. The pifi mutant exhibited a lower capacity for nonphotochemical quenching, but similar CO(2) assimilation rates, photosystem II (PSII) quantum efficiencies (PhiPSII), and reduction levels of the primary electron acceptor of PSII (1 - qL) as compared with the wild type. The pifi mutant grows normally under optimal conditions, but exhibits greater sensitivity to photoinhibition and long-term mild heat stress than wild-type plants, which is consistent with lower capacity of nonphotochemical quenching. We conclude that PIFI is a novel component essential for NDH-mediated nonphotochemical reduction of the PQ pool in chlororespiratory electron transport.

Cyanobacterial NADPH dehydrogenase complexes

Cyanobacteria possess functionally distinct multiple NADPH dehydrogenase (NDH-1) complexes that are essential to CO(2) uptake, photosystem-1 cyclic electron transport and respiration. The unique nature of cyanobacterial NDH-1 complexes is the presence of subunits involved in CO(2) uptake. Other than CO(2) uptake, chloroplastic NDH-1 complex has a similar role as cyanobacterial NDH-1 complexes in photosystem-1 cyclic electron transport and respiration (chlororespiration). In this mini-review we focus on the structure and function of cyanobacterial NDH-1 complexes and their phylogeny. The function of chloroplastic NDH-1 complex and characteristics of plants defective in NDH-1 are also described for comparison.

Large-Scale Analysis of Chlorophyll Fluorescence Kinetics in Synechocystis sp. PCC 6803: Identification of the Factors Involved in the Modulation of Photosystem Stoichiometry

Since chlorophyll fluorescence reflects the redox state of photosynthetic electron transport chain, monitoring of chlorophyll fluorescence has been successfully applied for the screening of photosynthesis-related genes. Here we report that the mutants having a defect in the regulation of photosystem stoichiometry could be identified through the simple comparison of the induction kinetics of chlorophyll fluorescence. We made a library containing 500 mutants in the cyanobacterium Synechocystis sp. PCC 6803 with transposon-mediated gene disruption, and the mutants were used for the measurement of chlorophyll fluorescence kinetics for 45 s. We picked up two genes, pmgA and sll1961, which are involved in the modulation of photosystem stoichiometry. The disruptants of the two genes share common characteristics in their fluorescence kinetics, and we searched for mutants that showed such characteristics. Out of six mutants identified so far, five showed a different photosystem stoichiometry under high-light conditions. Thus, categorization based on the similarity of fluorescence kinetics is an excellent way to identify the function of genes.

Cyclic electron transport around photosystem I: genetic approaches

The light reactions in photosynthesis convert light energy into chemical energy in the form of ATP and drive the production of NADPH from NADP+. The reactions involve two types of electron flow in the chloroplast. While linear electron transport generates both ATP and NADPH, photosystem I cyclic electron transport is exclusively involved in ATP synthesis. The physiological significance of photosystem I cyclic electron transport has been underestimated, and our knowledge of the machineries involved remains very limited. However, recent genetic approaches using Arabidopsis thaliana have clarified the essential functions of this electron flow in both photoprotection and photosynthesis. Based on several lines of evidence presented here, it is necessary to reconsider the fundamental mechanisms of chloroplast energetics.

Chlororespiratory reduction 6 is a novel factor required for accumulation of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis

The chloroplast NAD(P)H dehydrogenase (NDH) complex is involved in photosystem I cyclic electron transport and chlororespiration in higher plants. An Arabidopsis (Arabidopsis thaliana) chlororespiratory reduction 6 (crr6) mutant lacking NDH activity was identified by means of chlorophyll fluorescence imaging. Accumulation of the NDH complex was impaired in crr6. Physiological characterization of photosynthetic electron transport indicated the specific defect of the NDH complex in crr6. In contrast to the CRR7 protein that was recently identified as a potential novel subunit of the NDH complex by means of the same screening, the CRR6 protein was stable under the crr2 mutant background in which the NDH complex does not accumulate. The CRR6 gene (At2g47910) encodes a novel protein without any known motif. Although CRR6 does not have any transmembrane domains, it is localized in the thylakoid membrane fraction of the chloroplast. CRR6 is conserved in phototrophs, including cyanobacteria, from which the chloroplast NDH complex has evolutionally originated, but not in Chlamydomonas reinhardtii, in which the NDH complex is absent. We believe that CRR6 is a novel specific factor for the assembly or stabilization of the NDH complex.