Overexpression and characterization of dark-operative protochlorophyllide reductase from Rhodobacter capsulatus

Crystal structure and reaction mechanism of a bacterial Mg-dechelatase homolog from the Chloroflexi Anaerolineae

Chlorophyll degradation plays a myriad of physiological roles in photosynthetic organisms, including acclimation to light environment and nutrient remobilization during senescence. Mg extraction from chlorophyll a is the first and committed step of the chlorophyll degradation pathway. This reaction is catalyzed by the Mg-dechelatase enzyme encoded by Stay-Green (SGR). The reaction mechanism of SGR protein remains elusive since metal ion extraction from organic molecules is not a common enzymatic reaction. Additionally, experimentally derived structural information about SGR or its homologs has not yet been reported. In this study, the crystal structure of the SGR homolog from Anaerolineae bacterium was determined using the molecular replacement method at 1.85 Å resolution. Our previous study showed that three residues-H32, D34, and D62 are essential for the catalytic activity of the enzyme. Biochemical analysis involving mutants of D34 residue further strengthened its importance in the functioning of the dechelatase. Docking simulation also revealed the interaction between the D34 side chain and central Mg ion of chlorophyll a. Structural analysis showed the arrangement of D34/H32/D62 in the form of a catalytic triad that is generally found in hydrolases. The probable reaction mechanism suggests that deprotonated D34 side chain coordinates and destabilizes Mg, resulting in Mg extraction. Besides, H32 possibly acts as a general base catalyst and D62 facilitates H32 to be a better proton acceptor. Taken together, the reaction mechanism of SGR partially mirrors the one observed in hydrolases.

Regulation Mechanism of Exogenous Brassinolide on Bulbil Formation and Development in Pinellia ternata

The bulbil is the propagative organ of the P. ternata, which has a great effect on the yield of P. ternata. It is well known that plant hormones play important roles in bulbil formation and development. However, there is not clear about brassinolide (BR) regulation on bulbil formation and development. In this study, we revealed the effects of BR and BR biosynthesis inhibitors (propiconazole, Pcz) application on the histological observation, starch and sucrose metabolism, photosynthesis pathway, and hormone signaling pathway of P. ternata. The results showed that BR treatment reduced starch catabolism to maltodextrin and maltose in bulbil by decreasing BAM and ISA genes expression and increased cellulose catabolism to D-glucose in bulbil by enhancing edg and BGL genes expression. BR treatment enhanced the photosynthetic pigment content and potential maximum photosynthetic capacity and improved the photoprotection ability of P. ternata by increasing the dissipation of excess light energy to heat, thus reduced the photodamage in the PSII center. BR treatment increased the GA and BR content in bulbil of P. ternata, and decreased the ABA content in bulbil of P. ternata. Pcz treatment increased the level of GA, SL, ABA, and IAA in bulbil of P. ternata. BR regulated the signal transduction of BR, IAA, and ABA to regulate the formation and development of bulbil in P. ternata. These results provide molecular insight into BR regulation on bulbil formation and development.

Methods for Heterologous Overproduction of Fe-S Proteins

Proteins carrying iron-sulfur ([Fe-S]) clusters are critical to the basic metabolism of all organisms. Structural and biochemical investigations of many such [Fe-S] cluster proteins depend on recombinant overproduction using heterologous bacterial hosts such as Escherichia coli . Here, we describe a detailed procedure for the overproduction and purification of two oxygen-sensitive component proteins of the dark-operative protochlorophyllide oxidoreductase (DPOR) complex. The method relies on an engineered Escherichia coli cell line carrying a correction in its genome to restore the loss of a key [Fe-S] cluster biogenesis pathway. The method can also be potentially adapted for the overproduction of other Fe-S proteins.

Photosynthetic Metabolism and Nitrogen Reshuffling Are Regulated by Reversible Cysteine Thiol Oxidation Following Nitrogen Deprivation in Chlamydomonas

As global temperatures climb to historic highs, the far-reaching effects of climate change have impacted agricultural nutrient availability. This has extended to low latitude oceans, where a deficit in both nitrogen and phosphorus stores has led to dramatic decreases in carbon sequestration in oceanic phytoplankton. Although Chlamydomonas reinhardtii, a freshwater model green alga, has shown drastic systems-level alterations following nitrogen deprivation, the mechanisms through which these alterations are triggered and regulated are not fully understood. This study examined the role of reversible oxidative signaling in the nitrogen stress response of C. reinhardtii. Using oxidized cysteine resin-assisted capture enrichment coupled with label-free quantitative proteomics, 7889 unique oxidized cysteine thiol identifiers were quantified, with 231 significantly changing peptides from 184 proteins following 2 h of nitrogen deprivation. These results demonstrate that the cellular response to nitrogen assimilation, photosynthesis, pigment biosynthesis, and lipid metabolism are regulated by reversible oxidation. An enhanced role of non-damaging oxidative pathways is observed throughout the photosynthetic apparatus that provides a framework for further analysis in phototrophs.

Chlorophyllide a oxidoreductase Preferentially Catalyzes 8-Vinyl Reduction over B-Ring Reduction of 8-Vinyl Chlorophyllide a in the Late Steps of Bacteriochlorophyll Biosynthesis

Bacteriochlorophyll a (BChl) is an essential pigment for anoxygenic photosynthesis. In late steps of the BChl biosynthesis of Rhodobacter capsulatus, the C8 vinyl group and C7=C8 double bond of 8-vinyl chlorophyllide a (8 V-Chlide) are reduced by a C8 vinyl reductase (8VR), BciA, and a nitrogenase-like enzyme, chlorophyllide a oxidoreductase (COR), respectively, to produce 3-vinyl-bacteriochlorphyllide a. Recently, we discovered 8VR activity in COR. However, the kinetic parameters of the COR 8VR activity remain unknown, while those of the COR C7=C8 reductase activity and BciA have been reported. Here, we determined the kinetic parameters of COR 8VR activity by using 8 V-Chlide. The K_m value for 8 V-Chlide was 1.4 μM, which is much lower than the 6.2 μM determined for the C7=C8 reduction of Chlide. The kinetic parameters of the dual activities of COR suggest that COR catalyzes the reduction of the C8 vinyl group of 8 V-Chlide preferentially over C7=C8 reduction when both substrates are supplied during BChl biosynthesis.

Horizontal Transfer of Promiscuous Activity from Nonphotosynthetic Bacteria Contributed to Evolution of Chlorophyll Degradation Pathway

The relationship between enzymes and substrates does not perfectly match the "lock and key" model, because enzymes act on molecules other than their true substrate in different catalytic reactions. Such biologically nonfunctional reactions are called "promiscuous activities." Promiscuous activities are apparently useless, but they can be an important starting point for enzyme evolution. It has been hypothesized that enzymes with low promiscuous activity will show enhanced promiscuous activity under selection pressure and become new specialists through gene duplication. Although this is the prevailing scenario, there are two major problems: 1) it would not apply to prokaryotes because horizontal gene transfer is more significant than gene duplication and 2) there is no direct evidence that promiscuous activity is low without selection pressure. We propose a new scenario including various levels of promiscuous activity throughout a clade and horizontal gene transfer. STAY-GREEN (SGR), a chlorophyll a-Mg dechelating enzyme, has homologous genes in bacteria lacking chlorophyll. We found that some bacterial SGR homologs have much higher Mg-dechelating activities than those of green plant SGRs, while others have no activity, indicating that the level of promiscuous activity varies. A phylogenetic analysis suggests that a bacterial SGR homolog with high dechelating activity was horizontally transferred to a photosynthetic eukaryote. Some SGR homologs acted on various chlorophyll molecules that are not used as substrates by green plant SGRs, indicating that SGR acquired substrate specificity after transfer to eukaryotes. We propose that horizontal transfer of high promiscuous activity is one process of new enzyme acquisition.

Elevated Expression of a Functional Suf Pathway in Escherichia coli BL21(DE3) Enhances Recombinant Production of an Iron-Sulfur Cluster-Containing Protein

Structural and spectroscopic analysis of iron-sulfur [Fe-S] cluster-containing proteins is often limited by the occupancy and yield of recombinantly produced proteins. Here we report that Escherichia coli BL21(DE3), a strain routinely used to overproduce [Fe-S] cluster-containing proteins, has a nonfunctional Suf pathway, one of two E. coli [Fe-S] cluster biogenesis pathways. We confirmed that BL21(DE3) and commercially available derivatives carry a deletion that results in an in-frame fusion of sufA and sufB genes within the sufABCDSE operon. We show that this fusion protein accumulates in cells but is inactive in [Fe-S] cluster biogenesis. Restoration of an intact Suf pathway combined with enhanced suf operon expression led to a remarkable (∼3-fold) increase in the production of the [4Fe-4S] cluster-containing BchL protein, a key component of the dark-operative protochlorophyllide oxidoreductase complex. These results show that this engineered "SufFeScient" derivative of BL21(DE3) is suitable for enhanced large-scale synthesis of an [Fe-S] cluster-containing protein.IMPORTANCE Large quantities of recombinantly overproduced [Fe-S] cluster-containing proteins are necessary for their in-depth biochemical characterization. Commercially available E. coli strain BL21(DE3) and its derivatives have a mutation that inactivates the function of one of the two native pathways (Suf pathway) responsible for cluster biogenesis. Correction of the mutation, combined with sequence changes that elevate Suf protein levels, can increase yield and cluster occupancy of [Fe-S] cluster-containing enzymes, facilitating the biochemical analysis of this fascinating group of proteins.

Evolution of light-independent protochlorophyllide oxidoreductase

The nonhomologous enzymes, the light-independent protochlorophyllide reductase (DPOR) and the light-dependent protochlorophyllide oxidoreductase (LPOR), catalyze the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) in the penultimate step of biosynthesis of chlorophyll (Chl) required for photosynthetic light absorption and energy conversion. The two enzymes differ with respect to the requirement of light for catalysis and oxygen sensitivity. DPOR and LPOR initially evolved in the ancestral prokaryotic genome perhaps at different times. DPOR originated in the anoxygenic environment of the Earth from nitrogenase-like enzyme of methanogenic archaea. Due to the transition from anoxygenic to oxygenic photosynthesis in the prokaryote, the DPOR was mostly inactivated in the daytime by photosynthetic O₂ leading to the evolution of oxygen-insensitive LPOR that could function in the light. The primary endosymbiotic event transferred the DPOR and LPOR genes to the eukaryotic phototroph; the DPOR remained in the genome of the ancestor that turned into the plastid, whereas LPOR was transferred to the host nuclear genome. From an evolutionary point of view, several compelling theories that explain the disappearance of DPOR from several species cutting across different phyla are as follows: (i) pressure of the oxygenic environment; (ii) change in the light conditions and temperature; and (iii) lineage-specific gene losses, RNA editing, and nonsynonymous substitution. Certain primary amino acid sequence and the physiochemical properties of the ChlL subunit of DPOR have similarity with that of LPOR suggesting a convergence of these two enzymes in certain evolutionary event. The newly obtained sequence data from different phototrophs will further enhance the width of the phylogenetic information on DPOR.

The Effect of Two Amino acid Residue Substitutions via RNA Editing on Dark-operative Protochlorophyllide Oxidoreductase in the Black Pine Chloroplasts

Dark-operative protochlorophyllide oxidoreductase (DPOR) is a key enzyme to produce chlorophyll in the dark. Among photosynthetic eukaryotes, all three subunits chlL, chlN, and chlB are encoded by plastid genomes. In some gymnosperms, two codons of chlB mRNA are changed by RNA editing to codons encoding evolutionarily conserved amino acid residues. However, the effect of these substitutions on DPOR activity remains unknown. We first prepared cyanobacterial ChlB variants with amino acid substitution(s) to mimic ChlB translated from pre-edited mRNA. Their activities were evaluated by measuring chlorophyll content of dark-grown transformants of a chlB-lacking mutant of the cyanobacterium Leptolyngbya boryana that was complemented with pre-edited mimic chlB variants. The chlorophyll content of the transformant cells expressing the ChlB variant from the fully pre-edited mRNA was only one-fourth of the control cells. Co-purification experiments of ChlB with Strep-ChlN suggested that a stable complex with ChlN is greatly impaired in the substituted ChlB variant. We then confirmed that RNA editing efficiency was markedly greater in the dark than in the light in cotyledons of the black pine Pinus thunbergii. These results indicate that RNA editing on chlB mRNA is important to maintain appropriate DPOR activity in black pine chloroplasts.

Stoichiometry of ATP hydrolysis and chlorophyllide formation of dark-operative protochlorophyllide oxidoreductase from Rhodobacter capsulatus

Dark-operative protochlorophyllide (Pchlide) oxidoreductase (DPOR) is a nitrogenase-like enzyme catalyzing a reduction of the C17 = C18 double bond of Pchlide to form chlorophyllide a (Chlide) in bacteriochlorophyll biosynthesis. DPOR consists of an ATP-dependent reductase component, L-protein (a BchL dimer), and a catalytic component, NB-protein (a BchN-BchB heterotetramer). The L-protein transfers electrons to the NB-protein to reduce Pchlide, which is coupled with ATP hydrolysis. Here we determined the stoichiometry of ATP hydrolysis and the Chlide formation of DPOR. The minimal ratio of ATP to Chlide (ATP/2e(-)) was 4, which coincides with that of nitrogenase. The ratio increases with increasing molar ratio of L-protein to NB-protein. This profile differs from that of nitrogenase. These results suggest that DPOR has a specific intrinsic property, while retaining the common features shared with nitrogenase.

Broadened Substrate Specificity of 3-Hydroxyethyl Bacteriochlorophyllide a Dehydrogenase (BchC) Indicates a New Route for the Biosynthesis of Bacteriochlorophyll a

Bacteriochlorophyll a biosynthesis requires formation of a 3-hydroxyethyl group on pyrrole ring A that gets subsequently converted into a 3-acetyl group by 3-vinyl bacteriochlorophyllide a hydratase (BchF) followed by 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase (BchC). Heterologous overproduction of Chlorobaculum tepidum BchF revealed an integral transmembrane protein that was efficiently isolated by detergent solubilization. Recombinant C. tepidum BchC was purified as a soluble protein-NAD(+) complex. Substrate recognition of BchC was investigated using six artificial substrate molecules. Modification of the isocyclic E ring, omission of the central magnesium ion, zinc as an alternative metal ion, and a non-reduced B ring system were tolerated by BchC. According to this broadened in vitro activity, the chlorin 3-hydroxyethyl chlorophyllide a was newly identified as a natural substrate of BchC in a reconstituted pathway consisting of dark-operative protochlorophyllide oxidoreductase, BchF, and BchC. The established reaction sequence would allow for an additional new branching point for the synthesis of bacteriochlorophyll a. Biochemical and site-directed mutagenesis analyses revealed, in contrast to theoretical predictions, a zinc-independent BchC catalysis that requires NAD(+) as a cofactor. Based on these results, we are designating a new medium-chain dehydrogenase/reductase family (MDR057 BchC) as theoretically proposed from a recent bioinformatics analysis.

Iron-sulfur cluster-dependent catalysis of chlorophyllide a oxidoreductase from Roseobacter denitrificans

Bacteriochlorophyll a biosynthesis requires the stereo- and regiospecific two electron reduction of the C7-C8 double bond of chlorophyllide a by the nitrogenase-like multisubunit metalloenzyme, chlorophyllide a oxidoreductase (COR). ATP-dependent COR catalysis requires interaction of the protein subcomplex (BchX)2 with the catalytic (BchY/BchZ)2 protein to facilitate substrate reduction via two redox active iron-sulfur centers. The ternary COR enzyme holocomplex comprising subunits BchX, BchY, and BchZ from the purple bacterium Roseobacter denitrificans was trapped in the presence of the ATP transition state analog ADP·AlF4(-). Electron paramagnetic resonance experiments revealed a [4Fe-4S] cluster of subcomplex (BchX)2. A second [4Fe-4S] cluster was identified on (BchY/BchZ)2. Mutagenesis experiments indicated that the latter is ligated by four cysteines, which is in contrast to the three cysteine/one aspartate ligation pattern of the closely related dark-operative protochlorophyllide a oxidoreductase (DPOR). In subsequent mutagenesis experiments a DPOR-like aspartate ligation pattern was implemented for the catalytic [4Fe-4S] cluster of COR. Artificial cluster formation for this inactive COR variant was demonstrated spectroscopically. A series of chemically modified substrate molecules with altered substituents on the individual pyrrole rings and the isocyclic ring were tested as COR substrates. The COR enzyme was still able to reduce the B ring of substrates carrying modified substituents on ring systems A, C, and E. However, substrates with a modification of the distantly located propionate side chain were not accepted. A tentative substrate binding mode was concluded in analogy to the related DPOR system.

Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria

In all photosynthetic organisms, chlorophylls function as light-absorbing photopigments allowing the efficient harvesting of light energy. Chlorophyll biosynthesis recurs in similar ways in anoxygenic phototrophic proteobacteria as well as oxygenic phototrophic cyanobacteria and plants. Here, the biocatalytic conversion of protochlorophyllide to chlorophyllide is catalysed by evolutionary and structurally distinct protochlorophyllide reductases (PORs) in anoxygenic and oxygenic phototrophs. It is commonly assumed that anoxygenic phototrophs only contain oxygen-sensitive dark-operative PORs (DPORs), which catalyse protochlorophyllide reduction independent of the presence of light. In contrast, oxygenic phototrophs additionally (or exclusively) possess oxygen-insensitive but light-dependent PORs (LPORs). Based on this observation it was suggested that light-dependent protochlorophyllide reduction first emerged as a consequence of increased atmospheric oxygen levels caused by oxygenic photosynthesis in cyanobacteria. Here, we provide experimental evidence for the presence of an LPOR in the anoxygenic phototrophic α-proteobacterium Dinoroseobacter shibae DFL12(T). In vitro and in vivo functional assays unequivocally prove light-dependent protochlorophyllide reduction by this enzyme and reveal that LPORs are not restricted to cyanobacteria and plants. Sequence-based phylogenetic analyses reconcile our findings with current hypotheses about the evolution of LPORs by suggesting that the light-dependent enzyme of D. shibae DFL12(T) might have been obtained from cyanobacteria by horizontal gene transfer.

Dark-operative protochlorophyllide oxidoreductase generates substrate radicals by an iron-sulphur cluster in bacteriochlorophyll biosynthesis

Photosynthesis converts solar energy to chemical energy using chlorophylls (Chls). In a late stage of biosynthesis of Chls, dark-operative protochlorophyllide (Pchlide) oxidoreductase (DPOR), a nitrogenase-like enzyme, reduces the C17 = C18 double bond of Pchlide and drastically changes the spectral properties suitable for photosynthesis forming the parental chlorin ring for Chl a. We previously proposed that the spatial arrangement of the proton donors determines the stereospecificity of the Pchlide reduction based on the recently resolved structure of the DPOR catalytic component, NB-protein. However, it was not clear how the two-electron and two-proton transfer events are coordinated in the reaction. In this study, we demonstrate that DPOR initiates a single electron transfer reaction from a [4Fe-4S]-cluster (NB-cluster) to Pchlide, generating Pchlide anion radicals followed by a single proton transfer, and then, further electron/proton transfer steps transform the anion radicals into chlorophyllide (Chlide). Thus, DPOR is a unique iron-sulphur enzyme to form substrate radicals followed by sequential proton- and electron-transfer steps with the protein folding very similar to that of nitrogenase. This novel radical-mediated reaction supports the biosynthesis of Chl in a wide variety of photosynthetic organisms.

Carbon-carbon double-bond reductases in nature

Reduction of C = C bonds by reductases, found in a variety of microorganisms (e.g. yeasts, bacteria, and lower fungi), animals, and plants has applications in the production of metabolites that include pharmacologically active drugs and other chemicals. Therefore, the reductase enzymes that mediate this transformation have become important therapeutic targets and biotechnological tools. These reductases are broad-spectrum, in that, they can act on isolation/conjugation C = C-bond compounds, α,β-unsaturated carbonyl compounds, carboxylic acids, acid derivatives, and nitro compounds. In addition, several mutations in the reductase gene have been identified, some associated with diseases. Several of these reductases have been cloned and/or purified, and studies to further characterize them and determine their structure in order to identify potential industrial biocatalysts are still in progress. In this study, crucial reductases for bioreduction of C = C bonds have been reviewed with emphasis on their principal substrates and effective inhibitors, their distribution, genetic polymorphisms, and implications in human disease and treatment.

Chlorophyllide a oxidoreductase works as one of the divinyl reductases specifically involved in bacteriochlorophyll a biosynthesis

Bacteriochlorophyll a is widely distributed among anoxygenic photosynthetic bacteria. In bacteriochlorophyll a biosynthesis, the reduction of the C8 vinyl group in 8-vinyl-chlorophyllide a is catalyzed to produce chlorophyllide a by an 8-vinyl reductase called divinyl reductase (DVR), which has been classified into two types, BciA and BciB. However, previous studies demonstrated that mutants lacking the DVR still synthesize normal bacteriochlorophyll a with the C8 ethyl group and suggested the existence of an unknown "third" DVR. Meanwhile, we recently observed that chlorophyllide a oxidoreductase (COR) of a purple bacterium happened to show the 8-vinyl reduction of 8-vinyl-chlorophyllide a in vitro. In this study, we made a double mutant lacking BciA and COR of the purple bacterium Rhodobacter sphaeroides in order to investigate whether the mutant still produces pigments with the C8 ethyl group or if COR actually works as the third DVR. The single mutant deleting BciA or COR showed production of the C8 ethyl group pigments, whereas the double mutant accumulated 8-vinyl-chlorophyllide, indicating that there was no enzyme other than BciA and COR functioning as the unknown third DVR in Rhodobacter sphaeroides (note that this bacterium has no bciB gene). Moreover, some COR genes derived from other groups of anoxygenic photosynthetic bacteria were introduced into the double mutant, and all of the complementary strains produced normal bacteriochlorophyll a. This observation indicated that COR of these bacteria performs two functions, reductions of the C8 vinyl group and the C7=C8 double bond, and that such an activity is probably conserved in the widely ranging groups.

Nicotinamide is a specific inhibitor of dark-operative protochlorophyllide oxidoreductase, a nitrogenase-like enzyme, from Rhodobacter capsulatus

Dark-operative protochlorophyllide oxidoreductase (DPOR) is a nitrogenase-like enzyme consisting of two components, L-protein as a reductase component and NB-protein as a catalytic component. Elucidation of the crystal structures of NB-protein (Muraki et al., Nature 2010, 465: 110-114) has enabled us to study its reaction mechanism in combination with biochemical analysis. Here we demonstrate that nicotinamide (NA) inhibits DPOR activity by blocking the electron transfer from L-protein to NB-protein. A reaction scheme of DPOR, in which the binding of protochlorophyllide (Pchlide) to the NB-protein precedes the electron transfer from the L-protein, is proposed based on the NA effects.

Identification and molecular characterization of the second Chlamydomonas gun4 mutant, gun4-II

The green micro-alga Chlamydomonas reinhardtii is an elegant model organism to study oxygenic photosynthesis. Chlorophyll (Chl) and heme are major tetrapyrroles that play an essential role in photosynthesis and respiration. These tetrapyrroles are synthesized via a common branched pathway that involves mainly enzymes, encoded by nuclear genes. One of the enzymes in the pathway is Mg chelatase (MgChel). MgChel catalyzes insertion of Mg (2+) into protoporphyrin IX (PPIX, proto) to form Magnesium-protoporphyrin IX (MgPPIX, Mgproto), the first biosynthetic intermediate in the Chl branch. The GUN4 (genomes uncoupled 4) protein is not essential for the MgChel activity but has been shown to significantly stimulate its activity. We have isolated a light sensitive mutant, 6F14, by random DNA insertional mutagenesis. 6F14 cannot tolerate light intensities higher than 90-100 μmol photons m (-2) s (-1). It shows a light intensity dependent progressive photo-bleaching. 6F14 is incapable of photo-autotrophic growth under light intensity higher than 100 μmol photons m (-2) s (-1). PCR based analyses show that in 6F14 the insertion of the plasmid outside the GUN4 locus has resulted in a genetic rearrangement of the GUN4 gene and possible deletions in the genomic region flanking the GUN4 gene. Our gun4 mutant has a Chl content very similar to that in the wild type in the dark and is very sensitive to fluctuations in the light intensity in the environment unlike the earlier identified Chlamydomonas gun4 mutant. Complementation with a functional copy of the GUN4 gene restored light tolerance, Chl biosynthesis and photo-autotrophic growth under high light intensities in 6F14. 6F14 is the second gun4 mutant to be identified in C. reinhardtii. Additionally, we show that our two gun4 complements over-express the GUN4 protein and show a higher Chl content per cell compared to that in the wild type strain.

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ

The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/PrrA two-component system with a central role in redox regulation in R. sphaeroides. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA.

On the ATP-dependent activation of the radical enzyme (R)-2-hydroxyisocaproyl-CoA dehydratase

Members of the 2-hydroxyacyl-CoA dehydratase enzyme family catalyze the β,α-dehydration of various CoA-esters in the fermentation of amino acids by clostridia. Abstraction of the nonacidic β-proton of the 2-hydroxyacyl-CoA compounds is achieved by the reductive generation of ketyl radicals on the substrate, which is initiated by the transfer of an electron at low redox potentials. The highly energetic electron needed on the dehydratase is donated by a [4Fe-4S] cluster containing ATPase, termed activator. We investigated the activator of the 2-hydroxyisocaproyl-CoA dehydratase from Clostridium difficile. The activator is a homodimeric protein structurally related to acetate and sugar kinases, Hsc70 and actin, and has a [4Fe-4S] cluster bound in the dimer interface. The crystal structures of the Mg-ADP, Mg-ADPNP, and nucleotide-free states of the reduced activator have been solved at 1.6-3.0 Å resolution, allowing us to define the position of Mg(2+) and water molecules in the vicinity of the nucleotides and the [4Fe-4S] cluster. The structures reveal redox- and nucleotide dependent changes agreeing with the modulation of the reduction potential of the [4Fe-4S] cluster by conformational changes. We also investigated the propensity of the activator to form a complex with its cognate dehydratase in the presence of Mg-ADP and Mg-ADPNP and together with the structural data present a refined mechanistic scheme for the ATP-dependent electron transfer between activator and dehydratase.

Functional evaluation of a nitrogenase-like protochlorophyllide reductase encoded by the chloroplast DNA of Physcomitrella patens in the cyanobacterium Leptolyngbya boryana

Dark-operative protochlorophyllide (Pchlide) oxidoreductase (DPOR) is a nitrogenase-like enzyme consisting of the two components, L-protein (a ChlL dimer) and NB-protein (a ChlN-ChlB heterotetramer), to catalyze Pchlide reduction in Chl biosynthesis. While nitrogenase is distributed only among certain prokaryotes, the probable structural genes for DPOR are encoded by chloroplast DNA in lower plants. Here we show functional evaluation of DPOR encoded by chloroplast DNA in a moss Physcomitrella patens by the complementation analysis of the cyanobacterium Leptolyngbya boryana and the heterologous reconstitution of the moss L-protein and the cyanobacterial NB-protein. Two shuttle vectors to overexpress chlL and chlN-chlB from P. patens were introduced into the cyanobacterial chlL- and chlB-lacking mutants, respectively. Both transformants restored the ability to perform Chl biosynthesis in the dark, indicating that the chloroplast-encoded DPOR components form an active complex with the cyanobacterial components. The L-protein of P. patens was purified from the cyanobacterial transformant, and DPOR activity was reconstituted in a heterologous combination with the cyanobacterial NB-protein. The specific activity of the L-protein from P. patens was determined to be 118 nmol min(-1) mg (-1), which is even higher than that of the cyanobacterial L-protein (76 nmol min(-1) mg (-1)). Upon exposure to air, the activity of the L-protein from P. patens decayed with a half-life of 30 s, which was eight times faster than that of the cyanobacterial L-protein (240 s). These results suggested that the chloroplast-encoded L-protein functions as efficiently as the cyanobacterial L-protein but is more oxygen labile than the cyanobacterial L-protein.

EPR study of 1Asp-3Cys ligated 4Fe-4S iron-sulfur cluster in NB-protein (BchN-BchB) of a dark-operative protochlorophyllide reductase complex

Dark-operative protochlorophyllide oxidoreductase, a nitrogenase-like enzyme, contains two [4Fe-4S] clusters, one in the L-protein ((BchL)(2)) and the other in the NB-protein ((BchN-BchB)(2)). The reduced NB-cluster in the NB-protein, which is ligated by 1Asp/3Cys residues, showed a broad S=3/2 electron paramagnetic resonance signal that is rather rare in [4Fe-4S] clusters. A 4Cys-ligated NB-cluster in the mutated variant BchB-D36C protein, in which the Asp36 was replaced by a Cys, gave a rhombic normal S=1/2 signal and lost the catalytic activity. The results suggest that Asp36 contributes to the low redox potential necessary to reduce protochlorophyllide.

Chlorophyll biosynthesis: spotlight on protochlorophyllide reduction

Photosynthetic organisms require chlorophyll or bacteriochlorophyll for their light trapping and energy transduction activities. The biosynthetic pathways of chlorophyll and bacteriochlorophyll are similar in most of their early steps, except for the reduction of protochlorophyllide (Pchlide) to chlorophyllide. Whereas angiosperms make use of a light-dependent enzyme, cyanobacteria, algae, bryophytes, pteridophytes and gymnosperms contain an additional, light-independent enzyme dubbed dark-operative Pchlide oxidoreductase (DPOR). Anoxygenic photosynthetic bacteria such as Rhodobacter capsulatus and Rhodobacter sphaeroides rely solely on DPOR. Recent atomic resolution of reductase and catalytic components of DPOR from R. sphaeroides and R. capsulatus, respectively, have revealed their similarity to nitrogenase components. In this review, we discuss the two fundamentally different mechanisms of Pchlide reduction in photosynthetic organisms.

X-ray crystal structure of the light-independent protochlorophyllide reductase

Photosynthetic organisms adopt two different strategies for the reduction of the C17 = C18 double bond of protochlorophyllide (Pchlide) to form chlorophyllide a, the direct precursor of chlorophyll a (refs 1-4). The first involves the activity of the light-dependent Pchlide oxidoreductase, and the second involves the light-independent (dark-operative) Pchlide oxidoreductase (DPOR). DPOR is a nitrogenase-like enzyme consisting of two components, L-protein (a BchL dimer) and NB-protein (a BchN-BchB heterotetramer), which are structurally related to nitrogenase Fe protein and MoFe protein, respectively. Here we report the crystal structure of the NB-protein of DPOR from Rhodobacter capsulatus at a resolution of 2.3A. As expected, the overall structure is similar to that of nitrogenase MoFe protein: each catalytic BchN-BchB unit contains one Pchlide and one iron-sulphur cluster (NB-cluster) coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific Pchlide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit. We propose a unique trans-specific reduction mechanism in which the distorted C17-propionate of Pchlide and an aspartate from BchB serve as proton donors for C18 and C17 of Pchlide, respectively. Intriguingly, the spatial arrangement of the NB-cluster and Pchlide is almost identical to that of the P-cluster and FeMo-cofactor in nitrogenase MoFe-protein, illustrating that a common architecture exists to reduce chemically stable multibonds of porphyrin and dinitrogen.

The tetrapyrrole biosynthetic pathway and its regulation in Rhodobacter capsulatus

The purple anoxygenic photosynthetic bacterium Rhodobacter capsulatus is capable of growing in aerobic or anaerobic conditions, in the dark or using light, etc. Achieving versatile metabolic adaptations from respiration to photosynthesis requires the use of tetrapyrroles such as heme and bacteriochlorophyll, in order to carry oxygen, to transfer electrons, and to harvest light energy. A third tetrapyrrole, cobalamin (vitamin B(12)), is synthesized and used as a cofactor for many enzymes. Heme, bacteriochlorophyll, and vitamin B(12) constitute three major end products of the tetrapyrrole biosynthetic pathway in purple bacteria. Their respective synthesis involves a plethora of enzymes, several that have been characterized and several that are uncharacterized, as described in this review. To respond to changes in metabolic requirements, the pathway undergoes complex regulation to direct the flow of tetrapyrrole intermediates into a specific branch(s) at the expense of other branches of the pathway. Transcriptional regulation of the tetrapyrrole synthesizing enzymes by redox conditions and pathway intermediates is reviewed. In addition, we discuss the involvement of several transcription factors (RegA, CrtJ, FnrL, AerR, HbrL, Irr) as well as the role of riboswitches. Finally, the interdependence of the tetrapyrrole branches on each other synthesis is discussed.

Oxygen sensitivity of a nitrogenase-like protochlorophyllide reductase from the cyanobacterium Leptolyngbya boryana

Dark-operative protochlorophyllide (Pchlide) oxido-reductase (DPOR) is a nitrogenase-like enzyme that catalyzes Pchlide reduction, the penultimate step of chlorophyll a biosynthesis. DPOR is distributed widely among oxygenic phototrophs such as cyanobacteria, green algae and gymnosperms. To determine how DPOR operates in oxygenic photosynthetic cells, we constructed two shuttle vectors for overexpression of Strep-tagged L-protein (ChlL) and Strep-tagged NB-protein (ChlN-ChlB) in Leptolyngbya boryana (formerly Plectonema boryanum) and introduced them into mutants lacking chlL and chlB. Both transformants restored the ability to produce chlorophyll in the dark. The DPOR activity was reconstituted by L-protein and NB-protein purified from the transformants under anaerobic conditions. L-protein activity disappeared within 5 min of exposure to air while NB-protein activity persisted for >30 min in an aerobic condition, indicating that the L-protein of DPOR components is the primary target of oxygen in cyanobacterial cells. These results suggested that the DPOR from an oxygenic photosynthetic organism did not acquire oxygen tolerance during evolution; but that the cyanobacterial cell developed a mechanism to protect DPOR from oxygen.

Mutational analysis of three bchH paralogs in (bacterio-)chlorophyll biosynthesis in Chlorobaculum tepidum

The first committed step in the biosynthesis of (bacterio-)chlorophyll is the insertion of Mg2+ into protoporphyrin IX by Mg-chelatase. In all known (B)Chl-synthesizing organisms, Mg-chelatase is encoded by three genes that are homologous to bchH, bchD, and bchI of Rhodobacter spp. The genomes of all sequenced strains of green sulfur bacteria (Chlorobi) encode multiple bchH paralogs, and in the genome of Chlorobaculum tepidum, there are three bchH paralogs, denoted CT1295 (bchT), CT1955 (bchS), and CT1957 (bchH). Cba. tepidum mutants lacking one or two of these paralogs were constructed and characterized. All of the mutants lacking only one of these BchH homologs, as well as bchS bchT and bchH bchT double mutants, which can only produce BchH or BchS, respectively, were viable. However, attempts to construct a bchH bchS double mutant, in which only BchT was functional, were consistently unsuccessful. This result suggested that BchT alone is unable to support the minimal (B)Chl synthesis requirements of cells required for viability. The pigment compositions of the various mutant strains varied significantly. The BChl c content of the bchS mutant was only approximately 10% of that of the wild type, and this mutant excreted large amounts of protoporphyrin IX into the growth medium. The observed differences in BChl c production of the mutant strains were consistent with the hypothesis that the three BchH homologs function in end product regulation and/or substrate channeling of intermediates in the BChl c biosynthetic pathway.

Substrate recognition of nitrogenase-like dark operative protochlorophyllide oxidoreductase from Prochlorococcus marinus

Chlorophyll and bacteriochlorophyll biosynthesis requires the two-electron reduction of protochlorophyllide a ringDbya protochlorophyllide oxidoreductase to form chlorophyllide a. A light-dependent (light-dependent Pchlide oxidoreductase (LPOR)) and an unrelated dark operative enzyme (dark operative Pchlide oxidoreductase (DPOR)) are known. DPOR plays an important role in chlorophyll biosynthesis of gymnosperms, mosses, ferns, algae, and photosynthetic bacteria in the absence of light. Although DPOR shares significant amino acid sequence homologies with nitrogenase, only the initial catalytic steps resemble nitrogenase catalysis. Substrate coordination and subsequent [Fe-S] cluster-dependent catalysis were proposed to be unrelated. Here we characterized the first cyanobacterial DPOR consisting of the homodimeric protein complex ChlL(2) and a heterotetrameric protein complex (ChlNB)(2). The ChlL(2) dimer contains one EPR active [4Fe-4S] cluster, whereas the (ChlNB)(2) complex exhibited EPR signals for two [4Fe-4S] clusters with differences in their g values and temperature-dependent relaxation behavior. These findings indicate variations in the geometry of the individual [4Fe-4S] clusters found in (ChlNB)(2). For the analysis of DPOR substrate recognition, 11 synthetic derivatives with altered substituents on the four pyrrole rings and the isocyclic ring plus eight chlorophyll biosynthetic intermediates were tested as DPOR substrates. Although DPOR tolerated minor modifications of the ring substituents on rings A-C, the catalytic target ring D was apparently found to be coordinated with high specificity. Furthermore, protochlorophyllide a, the corresponding [8-vinyl]-derivative and protochlorophyllide b were equally utilized as substrates. Distinct differences from substrate binding by LPOR were observed. Alternative biosynthetic routes for cyanobacterial chlorophyll biosynthesis with regard to the reduction of the C8-vinyl group and the interconversion of a chlorophyll a/b type C7 methyl/formyl group were deduced.

Regulation and evolution of chlorophyll metabolism

Chlorophylls are the most abundant tetrapyrrole molecules essential for photosynthesis in photosynthetic organisms. After many years of intensive research, most of the genes encoding the enzymes for the pathway have been identified, and recently the underlying molecular mechanisms have been elucidated. These studies revealed that the regulation of chlorophyll metabolism includes all levels of control to allow a balanced metabolic flow in response to external and endogenous factors and to ensure adaptation to varying needs of chlorophyll during plant development. Furthermore, identification of biosynthetic genes from various organisms and genetic analysis of functions of identified genes enables us to predict the evolutionary scenario of chlorophyll metabolism. In this review, based on recent findings, we discuss the regulation and evolution of chlorophyll metabolism.

NB-protein (BchN-BchB) of dark-operative protochlorophyllide reductase is the catalytic component containing oxygen-tolerant Fe-S clusters

Dark-operative protochlorophyllide (Pchlide) oxidoreductase is a nitrogenase-like enzyme consisting of the two components, L-protein (BchL-dimer) and NB-protein (BchN-BchB-heterotetramer). Here, we show that NB-protein is the catalytic component with Fe-S clusters. NB-protein purified from Rhodobacter capsulatus bound Pchlide that was readily converted to chlorophyllide a upon the addition of L-protein and Mg-ATP. The activity of NB-protein was resistant to the exposure to air. A Pchlide-free form of NB-protein purified from a bchH-lacking mutant showed an absorption spectrum suggesting the presence of Fe-S centers. Together with the Fe and sulfide contents, these findings suggested that NB-protein carries two oxygen-tolerant [4Fe-4S] clusters.

ATP-driven reduction by dark-operative protochlorophyllide oxidoreductase from Chlorobium tepidum mechanistically resembles nitrogenase catalysis

During chlorophyll and bacteriochlorophyll biosynthesis in gymnosperms, algae, and photosynthetic bacteria, dark-operative protochlorophyllide oxidoreductase (DPOR) reduces ring D of aromatic protochlorophyllide stereospecifically to produce chlorophyllide. We describe the heterologous overproduction of DPOR subunits BchN, BchB, and BchL from Chlorobium tepidum in Escherichia coli allowing their purification to apparent homogeneity. The catalytic activity was found to be 3.15 nmol min(-1) mg(-1) with K(m) values of 6.1 microm for protochlorophyllide, 13.5 microm for ATP, and 52.7 microm for the reductant dithionite. To identify residues important in DPOR function, 21 enzyme variants were generated by site-directed mutagenesis and investigated for their metal content, spectroscopic features, and catalytic activity. Two cysteine residues (Cys(97) and Cys(131)) of homodimeric BchL(2) are found to coordinate an intersubunit [4Fe-4S] cluster, essential for low potential electron transfer to (BchNB)(2) as part of the reduction of the protochlorophyllide substrate. Similarly, Lys(10) and Leu(126) are crucial to ATP-driven electron transfer from BchL(2). The activation energy of DPOR electron transfer is 22.2 kJ mol(-1) indicating a requirement for 4 ATP per catalytic cycle. At the amino acid level, BchL is 33% identical to the nitrogenase subunit NifH allowing a first tentative structural model to be proposed. In (BchNB)(2), we find that four cysteine residues, three from BchN (Cys(21), Cys(46), and Cys(103)) and one from BchB (Cys(94)), coordinate a second inter-subunit [4Fe-4S] cluster required for catalysis. No evidence for any type of molybdenum-containing cofactor was found, indicating that the DPOR subunit BchN clearly differs from the homologous nitrogenase subunit NifD. Based on the available data we propose an enzymatic mechanism of DPOR.

Superoxide generation by chlorophyllide a reductase of Rhodobacter sphaeroides

Chlorophyllide a reductase of Rhodobacter sphaeroides, which were reconstituted with the purified subunits of BchX, BchY, and BchZ, reduced ring B of chlorophyllide a using NADH under anaerobic conditions. Interestingly, suppressor mutations rescuing the inability of R. sphaeroides Fe-SOD mutant to grow in succinate-based minimal medium were predominantly mapped to BchZ subunit of chlorophyllide a reductase. The enzyme is labile in the presence of O(2). However, it generates superoxide at low O(2). The enzymes reconstituted with BchX, BchY, and the mutein subunit of BchZ from suppressor mutants showed less activity not only for chlorophyllide a reduction but also for superoxide generation compared with the enzyme reconstituted with the wild-type subunits. BchX, which contains FMN, and BchY are iron-sulfur proteins, whereas BchZ is a hemoprotein containing b-type heme. Neither chlorophyllide a reduction nor superoxide generation was observed with the enzyme reconstituted with the wild-type subunits of BchX and BchY, and the apo-subunit of BchZ that had been refolded without heme, in which FMN of BchX was fully reduced. Thus, superoxide is generated not from FMN of BchX but from heme of BchZ. Consistently, the heme of BchZ muteins was half-reduced in its redox state compared with that of wild-type BchZ.

Chlorophyll Biosynthesis in Bacteria: The Origins of Structural and Functional Diversity

The use of photochemical reaction centers to convert light energy into chemical energy, chlorophototrophy, occurs in organisms belonging to only five eubacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, and Firmicutes. All chlorophototrophs synthesize two types of pigments: (a) chlorophylls and bacteriochlorophylls, which function in both light harvesting and uniquely in photochemistry; and (b) carotenoids, which function primarily as photoprotective pigments but can also participate in light harvesting. Although hundreds of carotenoids have been identified, only 12 types of chlorophylls (Chl a, b, d; divinyl-Chl a and b; and 8(1)-hydroxy-Chl a) and bacteriochlorophylls (BChl a, b, c, d, e, and g) are currently known to occur in bacteria. This review summarizes recent progress in the identification of genes and enzymes in the biosynthetic pathways leading to Chls and BChls, the essential tetrapyrrole cofactors of photosynthesis, and addresses the mechanisms for generating functional diversity for solar energy capture and conversion in chlorophototrophs.

Recent advances in chlorophyll biosynthesis

The importance of chlorophyll (Chl) to the process of photosynthesis is obvious, and there is clear evidence that the regulation of Chl biosynthesis has a significant role in the regulation of assembly of the photosynthetic apparatus. The understanding of Chl biosynthesis has rapidly advanced in recent years. The identification of genetic loci associated with each of the biochemical steps has been accompanied by a greater appreciation of the role of Chl biosynthesis intermediates in intracellular signaling. The purpose of this review is to provide a source of information for all the steps in Chl and bacteriochlorophyll a biosynthesis, with an emphasis on steps that are believed to be key regulation points.

Nitrogenase Fe protein-like Fe-S cluster is conserved in L-protein (BchL) of dark-operative protochlorophyllide reductase fromRhodobacter capsulatus

Dark-operative protochlorophyllide reductase (DPOR) in bacteriochlorophyll biosynthesis is a nitrogenase-like enzyme consisting of L-protein (BchL-dimer) as a reductase component and NB-protein (BchN-BchB-heterotetramer) as a catalytic component. Metallocenters of DPOR have not been identified. Here we report that L-protein has an oxygen-sensitive [4Fe-4S] cluster similar to nitrogenase Fe protein. Purified L-protein from Rhodobacter capsulatus showed absorption spectra and an electron paramagnetic resonance signal indicative of a [4Fe-4S] cluster. The activity quickly disappeared upon exposure to air with a half-life of 20s. These results suggest that the electron transfer mechanism is conserved in nitrogenase Fe protein and DPOR L-protein.

A second nitrogenase-like enzyme for bacteriochlorophyll biosynthesis: reconstitution of chlorophyllide a reductase with purified X-protein (BchX) and YZ-protein (BchY-BchZ) from Rhodobacter capsulatus

In most photosynthetic organisms, the chlorin ring structure of chlorophyll a is formed by the reduction of the porphyrin D-ring by the dark-operative nitrogenase-like enzyme, protochlorophyllide reductase (DPOR). Subsequently, the chlorin B-ring is reduced in bacteriochlorophyll biosynthesis to form a bacteriochlorin ring structure. Phenotypic analysis of mutants lacking one of three genes, bchX, bchY, or bchZ, which show significant sequence similarity to the structural genes of nitrogenase, suggests that a second nitrogenase-like enzyme is involved in the chlorin B-ring reduction. However, there is no biochemical evidence for this. Here, we report the reconstitution of chlorophyllide a reductase (COR) with purified proteins. Two Rhodobacter capsulatus strains that overexpressed Strep-tagged BchX and BchY were isolated. Strep-tagged BchX was purified as a single polypeptide, and BchZ was co-purified with Strep-tagged BchY. When BchX and BchY-BchZ components were incubated with chlorophyllide a, ATP, and dithionite under anaerobic conditions, chlorophyllide a was converted to a new pigment with a Qy band of longer wavelength at 734 nm (P734) in 80% acetone. The formation of P734 was dependent on ATP and dithionite. High performance liquid chromatography and mass spectroscopic analysis indicated that P734 is 3-vinyl bacteriochlorophyllide a, which is formed by the B-ring reduction of chlorophyllide a. These results demonstrate that the B-ring of chlorin is reduced by a second nitrogenase-like enzyme and that the sequential actions of two nitrogenase-like enzymes, DPOR and COR, convert porphyrin to bacteriochlorin. The evolutionary implications of nitrogenase-like enzymes to determine the ring structure of (bacterio)chlorophyll pigments are discussed.

Making light work of enzyme catalysis: protochlorophyllide oxidoreductase

In the chlorophyll biosynthetic pathway, the enzyme protochlorophyllide oxidoreductase (POR) catalyses a key light-driven reaction that triggers a profound transformation in plant development. Because POR is activated by light, it can provide information on the way in which light energy can be harnessed to power enzyme reactions and it presents us with a unique opportunity to study catalysis at low temperatures and on ultrafast timescales that are not accessible for most analyses of enzyme function. Recent advances in our understanding of the catalytic mechanism of POR illustrate why it is an important generic model for studying enzyme catalysis and reaction dynamics.