In vitro synthesis of chloroplast ferredoxin as a high molecular weight precursor in a cell-free protein synthesizing system from wheat germs

Identification of global ferredoxin interaction networks in Chlamydomonas reinhardtii

Ferredoxins (FDXs) can distribute electrons originating from photosynthetic water oxidation, fermentation, and other reductant-generating pathways to specific redox enzymes in different organisms. The six FDXs identified in Chlamydomonas reinhardtii are not fully characterized in terms of their biological function. In this report, we present data from the following: (a) yeast two-hybrid screens, identifying interaction partners for each Chlamydomonas FDX; (b) pairwise yeast two-hybrid assays measuring FDX interactions with proteins from selected biochemical pathways; (c) affinity pulldown assays that, in some cases, confirm and even expand the interaction network for FDX1 and FDX2; and (d) in vitro NADP(+) reduction and H2 photo-production assays mediated by each FDX that verify their role in these two pathways. Our results demonstrate new potential roles for FDX1 in redox metabolism and carbohydrate and fatty acid biosynthesis, for FDX2 in anaerobic metabolism, and possibly in state transition. Our data also suggest that FDX3 is involved in nitrogen assimilation, FDX4 in glycolysis and response to reactive oxygen species, and FDX5 in hydrogenase maturation. Finally, we provide experimental evidence that FDX1 serves as the primary electron donor to two important biological pathways, NADPH and H2 photo-production, whereas FDX2 is capable of driving these reactions at less than half the rate observed for FDX1.

Formation of the iron-sulfur cluster of ferredoxin in isolated chloroplasts

The formation of the iron-sulfur cluster of ferredoxin was examined in vitro by incubating isolated chloroplasts with [(35)S]cysteine. The ferredoxin molecule was radioactively labeled in chloroplasts without synthesis of its polypeptide and comigrated with holoferredoxin during polyacrylamide gel electrophoresis under nondenaturing conditions. When the labeled ferredoxin was denatured by the addition of trichloroacetic acid, radioactive acid-labile sulfide in the cluster was released from the polypeptide as a gas and trapped in a 0.1 M NaOH solution. These results indicate that the sulfur atom derived from cysteine was incorporated into ferredoxin through formation of the iron-sulfur cluster. This process was stimulated by light and inhibited by the electron transport inhibitor, dichlorophenyldimethylurea, and the uncouplers, atebrin and gramicidin, but not by the protein synthesis inhibitor, chloramphenicol. These inhibitory effects were reversed by the addition of ATP to the incubation mixture. Formation of the iron-sulfur cluster of ferredoxin in chloroplasts is thus dependent on ATP.

Electrostatic interaction of phytochromobilin synthase and ferredoxin for biosynthesis of phytochrome chromophore

In plants, phytochromobilin synthase (HY2) synthesize the open chain tetrapyrrole chromophore for light-sensing phytochromes. It catalyzes the double bond reduction of a heme-derived tetrapyrrole intermediate biliverdin IXalpha (BV) at the A-ring diene system. HY2 is a member of ferredoxin-dependent bilin reductases (FDBRs), which require ferredoxins (Fds) as the electron donors for double bond reductions. In this study, we investigated the interaction mechanism of FDBRs and Fds by using HY2 and Fd from Arabidopsis thaliana as model proteins. We found that one of the six Arabidopsis Fds, AtFd2, was the preferred electron donor for HY2. HY2 and AtFd2 formed a heterodimeric complex that was stabilized by chemical cross-linking. Surface-charged residues on HY2 and AtFd2 were important in the protein-protein interaction as well as BV reduction activity of HY2. These surface residues are close to the iron-sulfur center of Fd and the HY2 active site, implying that the interaction promotes direct electron transfer from the Fd to HY2-bound BV. In addition, the C12 propionate group of BV is important for HY2-catalyzed BV reduction. A possible role for this functional group is to mediate the electron transfer by interacting directly with AtFd2. Together, our biochemical data suggest a docking mechanism for HY2:BV and AtFd2.

A post genomic characterization of Arabidopsis ferredoxins

In higher plant plastids, ferredoxin (Fd) is the unique soluble electron carrier protein located in the stroma. Consequently, a wide variety of essential metabolic and signaling processes depend upon reduction by Fd. The currently available plant genomes of Arabidopsis and rice (Oryza sativa) contain several genes encoding putative Fds, although little is known about the proteins themselves. To establish whether this variety represents redundancy or specialized function, we have recombinantly expressed and purified the four conventional [2Fe-2S] Fd proteins encoded in the Arabidopsis genome and analyzed their physical and functional properties. Two proteins are leaf type Fds, having relatively low redox potentials and supporting a higher photosynthetic activity. One protein is a root type Fd, being more efficiently reduced under nonphotosynthetic conditions and supporting a higher activity of sulfite reduction. A further Fd has a remarkably positive redox potential and so, although redox active, is limited in redox partners to which it can donate electrons. Immunological analysis indicates that all four proteins are expressed in mature leaves. This holistic view demonstrates how varied and essential soluble electron transfer functions in higher plants are fulfilled through a diversity of Fd proteins.

Comparison of the Nucleotide Sequences of Ferredoxin-cDNAs among some Datura Plants

The nucleotide sequences of partial ferredoxin (Fd)-cDNAs (corresponding to the amino acid sequence of 22-87 in the total 97 amino acids of ferredoxin) were determined for Datura arborea, D. stramonium, D. metel, and related Datura plants. Non-synonymous substitutions were noted at 4 positions and a synonymous substitution was seen at position 82 (Gln [CAA] (arborea) vs. Gln [CAG] (stramonium and metel)). The nucleotide sequence of Fd-cDNA may provide more detailed information regarding the relative taxonomic positions of plants than the amino acid sequence. However, Datura plants in the same section (metel, fastuosa, and innoxia) and of different varieties (stramonium var. stramonium and stramonium var. tatula) showed identical Fd-cDNA nucleotide sequences. This result suggests that there are very close relationships among the plants in each group.

Development of an ELISA approach for the determination of flavodoxin and ferredoxin as markers of iron deficiency in phytoplankton

Quantification of the iron-nutritional status of phytoplankton is of great interest not only for the study of oceans but also for fresh waters. Flavodoxin is a small flavoprotein proposed as a marker for iron deficiency, since it is induced as a consequence of iron deprivation, replacing the iron-sulphur protein ferredoxin. Flavodoxin and ferredoxin have been frequently used as markers for determination of iron deficiency in phytoplankton. Using purified flavodoxin and ferredoxin from Scenedesmus vacuolatus and polyclonal antibodies against both proteins, individual ELISA tests have been developed. The assays have a linear response in the range of 30-600 ng/ml of protein.

Crystal structure determination at 1.4 A resolution of ferredoxin from the green alga Chlorella fusca

BACKGROUND

[2Fe-2S] ferredoxins, also called plant-type ferredoxins, are low-potential redox proteins that are widely distributed in biological systems. In photosynthesis, the plant-type ferredoxins function as the central molecule for distributing electrons from the photolysis of water to a number of ferredox-independent enzymes, as well as to cyclic photophosphorylation electron transfer. This paper reports only the second structure of a [2Fe-2S] ferredoxin from a eukaryotic organism in its native form.

RESULTS

Ferredoxin from the green algae Chlorella fusca has been purified, characterised, crystallised and its structure determined to 1.4 A resolution - the highest resolution structure published to date for a plant-type ferredoxin. The structure has the general features of the plant-type ferredoxins already described, with conformational differences corresponding to regions of higher mobility. Immunological data indicate that a serine residue within the protein is partially phosphorylated. A slightly electropositive shift in the measured redox potential value, -325 mV, is observed in comparison with other ferredoxins.

CONCLUSIONS

This high-resolution structure provides a detailed picture of the hydrogen-bonding pattern around the [2Fe-2S] cluster of a plant-type ferredoxin; for the first time, it was possible to obtain reliable error estimates for the geometrical parameters. The presence of phosphoserine in the protein indicates a possible mechanism for the regulation of the distribution of reducing power from the photosynthetic electron-transfer chain.

Analysis of the gene cluster encoding toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1

The toluene/o-xylene monooxygenase cloned from Pseudomonas stutzeri OX1 displays a very broad range of substrates and a very peculiar regioselectivity, because it is able to hydroxylate more than one position on the aromatic ring of several hydrocarbons and phenols. The nucleotide sequence of the gene cluster coding for this enzymatic system has been determined. The sequence analysis revealed the presence of six open reading frames (ORFs) homologous to other genes clustered in operons coding for multicomponent monooxygenases found in benzene- and toluene-degradative pathways cloned from Pseudomonas strains. Significant similarities were also found with multicomponent monooxygenase systems for phenol, methane, alkene, and dimethyl sulfide cloned from different bacterial strains. The knockout of each ORF and complementation with the wild-type allele indicated that all six ORFs are essential for the full activity of the toluene/o-xylene monooxygenase in Escherichia coli. This analysis also shows that despite its activity on both hydrocarbons and phenols, toluene/ o-xylene monooxygenase belongs to a toluene multicomponent monooxygenase subfamily rather than to the monooxygenases active on phenols.

Characterization of the import process of a transit peptide into chloroplasts

In order to get insight into the functioning of transit sequences in chloroplast protein transport, the import of the full-length transit peptide of ferredoxin (trfd) was investigated. trfd rapidly associated with chloroplasts under import conditions and becomes protected against externally added proteases. Import of radiolabeled trfd is inhibited equally efficiently by nonlabeled trfd as well as by the intact precursor of ferredoxin. This strongly suggests that trfd enters the general import pathway of proteins into chloroplasts. trfd import was stimulated by ATP, which is the first demonstration that ATP is involved in membrane translocation of a targeting signal. Imported trfd was membrane-associated but was also partially degraded by internal proteases, most likely present in the stroma, indicating that the membrane-associated fraction of trfd is en route to its functional localization. The degradation products are exported out of the organelle. In contrast to the import of the precursor of ferredoxin, the import of trfd was independent of protease-sensitive components on the chloroplast surface, indicating that the initial binding of precursor proteins may be facilitated by transit sequence-lipid interactions.

The specificity of glycolipid-preferredoxin interaction: requirements for membrane binding

Preferredoxin (prefd) is a precursor protein that is imported into chloroplasts. Monolayer experiments have shown that prefd has a high affinity for monogalactosyldiglyceride (MGaIDG) isolated from chloroplasts, which contains polyunsaturated fatty acid constituents and is therefore in a liquid-expanded state, but has been found to interact also with MGaIDG with long-chain saturated fatty acids, which exist in a gel state. For an optimal interaction, the fatty acid chain length and the extent of unsaturation are also important parameters, whereas the conformation of the sugar moiety, the sugar-glycerol or glycerol-hydrocarbon chain linkages are of little influence on the pressure changes measured in monomolecular layers. Conversely, steric hindrance of a methyl group at position 3 of the sugar largely inhibits the interaction. Quantification of the interaction with radiolabelled prefd shows that only a small part of the molecule is able to penetrate MGaIDG in the gel state, whereas a nearly four-times larger part is able to penetrate MGaIDG isolated from chloroplasts. It is likely that interactions of the transit sequence of prefd with the glycolytic head group MGaIDG are involved in targeting and binding to the chloroplast membrane.

Developmental, circadian and light regulation of wheat ferredoxin gene expression

A genomic clone encoding the precursor of wheat leaf ferredoxin has been isolated and characterised. The uninterrupted PetF gene encodes a polypeptide of 143 amino acid residues, consisting of an N-terminal presequence of 46 amino acid residues and a mature polypeptide of 97 amino acid residues. Southern blot analysis suggests that six copies of the PetF gene are present in the wheat haploid genome. Northern blot analysis has shown that the genes are both developmentally and light regulated in wheat seedlings and provides evidence that a circadian rhythm regulates the steady-state levels of ferredoxin transcripts. The intact wheat gene and several chimeric constructs, containing portions of the 5'-upstream region fused to the beta-glucuronidase reporter gene, have been introduced into tobacco plants, but levels of beta-glucuronidase activity above background were not detected, suggesting that the 5'-upstream region is unable to function as a promoter in tobacco plants.

Regulation of synthesis of nitrite reductase in pea leaves: in-vivo and in-vitro studies

Crude protein extracts from leaves of pea (Pisum sativum L.) labeled with an L-(14)C-amino-acid mixture or [(35)S]methionine, were treated with antibodies prepared against nitrite reductase (NiR; EC 1.6.6.4). When the immunoprecipitates were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) a polypeptide with the same mobility as that of the native NiR was detected. By using darkened or illuminated leaves in the absence or presence of nitrate, it has been confirmed that nitrate is required in the in-vivo synthesis of NiR and that this synthesis is stimulated by light. Cell-free translation with a wheat-germ extract primed with polysomes from illuminated leaves treated with nitrate yielded polypeptides of a wide range of molecular weights (Mrs). Two polypeptides were immunoprecipitated from the translational products by anti-NiR serum. The mobility of one of them on SDS-PAGE corresponded to that of NiR while the other had a slightly higher Mr. It is concluded that NiR is synthesized as a heavy-molecular-weight precursor. Nitrate appears to regulate NiR synthesis by triggering transcription whereas the light may control the level of transcription or translation.

The plant ferredoxin precursor: nucleotide sequence of a full length cDNA clone

A cDNA clone (pFD1) derived from Silene pratensis ferredoxin mRNA was selected from a cDNA-library using the hybrid released translation technique. Nucleotide sequence analysis showed the cDNA insert to contain the complete coding region of the ferredoxin precursor protein. The ferredoxin precursor has a mol.wt. of 15 300, the transit-peptide has a mol.wt. of 5600. The length of the ferredoxin mRNA was found to be 700 nucleotides whereas the cDNA insert was about 1200 basepairs. S1 nuclease protection experiments showed the ferredoxin-specific DNA to be 660 basepairs in length and to start 39 nucleotides upstream of the ferredoxin coding sequence. Southern blot analysis of genomic DNA revealed the presence of only one fragment with homology to the ferredoxin cDNA probe, so it is probably a single-copy gene. Comparison of the ferredoxin transit-sequence with transit sequences of another stromal protein, the small subunit of ribulosebisphosphate carboxylase showed no apparent homology, except for a stretch of three amino acids near the processing site.

Chloroplast ribosomal proteins of Chlamydomonas synthesized in the cytoplasm are made as precursors

Polyadenylated RNA from Chlamydomonas was translated in a cell-free rabbit reticulocyte system that employed [35S]methionine. Antibodies made to four chloroplast ribosomal proteins synthesized in the cytoplasm and imported into the organelle were used for indirect immunoprecipitation of the labeled translation products, which were subsequently visualized on fluorographs of SDS gels. The cytoplasmically synthesized chloroplast ribosomal proteins were first seen as precursors with apparent molecular weights of 1,000 to 6,000 greater than their respective mature forms. Processing of the ribosomal protein precursors to mature proteins was affected by adding a postribosomal supernatant that had been extracted from cells of Chlamydomonas. In contrast to the chloroplast ribosomal proteins synthesized in the cytoplasm, two such proteins made within the chloroplast were found to be synthesized in mature form in cell-free wheat germ translation systems programmed with nonpolyadenylated RNA.

Phytoferritin is synthesized in vitro as a high-molecular-weight precursor. Studies on the synthesis and the uptake in vitro of the precursors of ferritin and ferredoxin by intact chloroplasts

Evidence is presented that French-bean (Phaseolus vulgaris) seed ferritin is composed of one type of subunit with an apparent Mr of 26500. In normal and iron-loaded leaf tissues it is detected immunologically with an antiserum raised against purified bean seed ferritin and migrates in SDS (sodium dodecyl sulphate)/polyacrylamide-gel electrophoresis with the same mobility as the bean seed ferritin subunit. The biosynthetic pathway of ferritin in normal and iron-loaded leaves was investigated. RNA was extracted, fractionated into polyadenylated RNA and translated in a cell-free rabbit reticulocyte lysate and a wheat-germ-extract system. The products were identified by SDS/polyacrylamide-gel electrophoresis after indirect immunoprecipitation. In all cases the ferritin product had an Mr 5000 higher than that of the native subunit. Uptake and processing of the precursor form of ferritin from iron-loaded leaves by intact chloroplasts was demonstrated. This indicates that, in iron-loaded leaves, ferritin acts as a chloroplast protein. We propose that the ferritin precursor in normal leaves follows the same biosynthetic pathway. This suggests that the iron-buffering function of ferritin in plants takes place in the chloroplast and that non-functional cellular iron will accumulate in this cell organelle.

The presence and synthesis of the NADPH-protochlorophyllide oxidoreductase in barley leaves with a high temperature-induced deficiency of plastid ribosomes

High-temperature-induced deficiency of plastid ribosomes in barley plants (Hordeum vulgare L.) was used as a system for studying the role of the cytoplasm in the synthesis of the NADPH-protochlorophyllide oxidoreductase. The enzyme is present in 33° C-grown plants. The failure of high-temperature-grown plants to accumulate chlorophyll during illumination is not caused by the absence of the protochlorophyllide-reducing enzyme. The synthesis of the NADPH-protochlorophyllide oxidoreductase was studied by feeding [(35)S]methionine to the seedling and by following the incorporation of the radioactively labeled amino acid into plastid proteins. The NADPH-protochlorophyllide oxidoreductase was labeled in high-temperature-grown barley plants to the same extent as in control plants grown at 25° C. It is concluded that the 36,000-Mr polypeptide of the NADPH-protochlorophyllide oxidoreductase is synthesized outside the plastid on cytoplasmic 80S ribosomes.

The protochlorophyllide holochrome of barley (Hordeum vulgare L.). Phytochrome-induced decrease of translatable mRNA coding for the NADPH: protochlorophyllide oxidoreductase

During the illumination of dark-grown barley plants light induces a rapid decrease of a translatable mRNA which codes for a polypeptide of Mr 44000. This component was identified as a precursor of the NADPH:protochlorophyllide oxidoreductase. The precursor has an Mr larger than the authentic protein by approximately 8000. The light-induced change in the level of translatable mRNA can be induced by a 15-s red-light pulse followed by 5 h of darkness. The red-light effect is reversed by a subsequent far-red-light treatment. It is concluded that the light-induced decline of translatable mRNA for the NADPH:protochlorophyllide oxidoreductase is controlled by phytochrome. The significance of this finding for present concepts of light-dependent control of chloroplast development and chlorophyll synthesis is discussed.

Genetic and biochemical implications of the endosymbiotic origin of the chloroplast

The hypothesis stating that chloroplasts were derived from a photosynthetic procaryote is explored at a genetic and biochemical level. A transfer of genetic material from the endosymbiont to the nucleus of the host cell is proposed along with a corollary argument that the protein products of such transferred genes have remained specific to the chloroplast. This model provides an explanation for the presence of plastid-specific isozymes which are coded by nuclear DNA. It also suggests that the genome of the endosymbiont contributed the information necessary for the biosynthesis of carotenoids and the "essential" amino acids and the assimilation of nitrate-nitrogen and sulfate-sulfur. Animal cells lack these capabilities not because such were lost subsequent to the divergence of the plant and animal lines, but because animal cells did not become host to the appropriate symbionts. Additional implications of this thesis are discussed.

Cell-free synthesis of the myelin basic proteins in a wheat germ system programmed with brain messenger RNA

Poly A(+) messenger RNA (mRNA) was isolated from the brains of 3-week-old mice and translated in a cell-free system derived from wheat germ. Maximal stimulation of the system by brain mRNA was observed at a relatively low K+ concentration (45 mM) and low mRNA concentration (1-10 microgram/ml). The translational system was dependent on an energy-generating system and stimulated by the addition of spermidine and transfer RNA. Under optimal conditions, incorporation was linear for almost 45 min, but the overall stimulation with brain mRNA was relatively low (about twofold). In spite of the low stimulation, analysis of the translation products indicated that in the presence of brain mRNA polypeptides which co-chromatographed and co-electrophoresed with the two mouse myelin basic proteins could be detected. In control experiments with liver poly A(+) mRNA, which stimulated the translational system to a greater extent than brain mRNA, no such polypeptides could be detected. In this system the ratio of synthesis of small myelin basic protein to large myelin basic protein was found to be about 4.0, which correlates well with that found in vivo.

Translation of poly-A RNA from rat liver in vitro. Evidence for a high molecular weight subunit of tyrosine aminotransferase

Poly-A RNA extracted from the rat liver was translated in a cell-free wheat germ system and a rabbit reticulocyte lysate. The subunit of tryptophan pyrrolase precipitated by specific antiserum after synthesis in vitro has the same molecular weight as the corresponding subunit derived from the rat liver. With specific antiserum prepared against tyrosine aminotransferase, however, a radioactive protein from both the in vitro assays was precipitated with an about 5% higher molecular weight than the tyrosine aminotransferase subunit precipitated from rat liver. The immunological evidence and the comparison of the specific peptide patterns prepared by cyanogen bromide treatment showed that the in vitro product corresponds to tyrosine aminotransferase. Various concentrations of potassium or spermidine used in the wheat germ translation system did not alter the size of the enzyme subunit synthesized. The run of the tyrosine aminotransferase purified form the rat liver in the SDS-polyacrylamide gel electrophoresis was not influenced by treatment with Escherichia coli alkaline phosphatase. The possibility is discussed that the larger enzyme synthesized in vitro represents a precursor molecule which is cleaved proteolytically in vivo.

Synthesis of cytochrome f by isolated pea chloroplasts

Chloroplasts, isolated from the leaves of 7-day-old pea seedlings, were incubated in the light with [35S]methionine or [3H]leucine. After extraction from the washed chloroplast membranes using a mixture of ethyl acetate, ethanol and ammonia, cytochrome f was precipitated with a monospecific antiserum and resolved by gradient polyacrylamide gel electrophoresis in sodium dodecylsulphate. The cytochrome f band was identified by its intrinsic fluorescence in ultraviolet light and was shown to be radioactive by autoradiography or fluorography of dried polyacrylamide gel. One-dimensional peptide mapping of the products of papain hydrolysis confirmed that the radioactivity was an integral part of cytochrome f. The incorporation of [35S]methionine into cytochrome f was inhibited by D(-)threo-chloramphenicol but not by cycloheximide and did not occur in the dark. The synthesis was resistant to ribonuclease. It is concluded that cytochrome f is synthesised in intact isolated pea chloroplasts.