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.     

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.     

Chlorophyll breakdown in oilseed rape

Chlorophyll catabolism accompanying leaf senescence is one of the most spectacular natural phenomena. Despite this fact, the metabolism of chlorophyll has been largely neglegted until recently. Oilseed rape has been used extensively as a model plant for the recent elucidating of structures of chlorophyll catabolites and for investigation of the enzymic reactions of the chlorophyll breakdown pathway. The key reaction which causes loss of green color is catalyzed in a two-step reaction by pheophorbide a oxygenase and red chlorophyll catabolite reductase. In this Minireview, we summarize the actual knowledge about catabolites and enzymes of chlorophyll catabolism in oilseed rape and discuss the significance of this pathway in respect to chlorophyll degradation during Brassica napus seed development. This revised version was published online in June 2006 with corrections to the Cover Date.     

Structure and function of glutamyl-tRNA reductase,the first enzyme of tetrapyrrole biosynthesis in plants and prokaryotes

Glutamyl-tRNA reductase (GluTR) catalyzes the first step of tetrapyrrole biosynthesis in plants, archaea and most bacteria. The catalytic mechanism of the enzyme was elucidated both by biochemical data and the determination of the high-resolution crystal structure of the enzyme from the archaeon Methanopyrus kandleri in complex with a competitive inhibitor. The dimeric enzyme has an unusual V-shaped architecture where each monomer consists of three domains linked by a long `spinal' α-helix. The central catalytic domain specifically recognizes the glutamate moiety of the substrate. It bears a conserved cysteine poised to nucleophilically attack the activated aminoacyl bond of glutamyl-tRNA. Subsequently, the thioester intermediate is reduced to the product glutamate-1-semialdehyde via hydride transfer from NADPH supplied by the second domain. A structure-based sequence alignment indicates that catalytically essential amino acids are conserved throughout all GluTRs. Thus the catalytic mechanism derived for M. kandleri is common to all including plant GluTRs. Mutations described to influence the catalytic efficiency of the barley enzyme can therefore be explained. This revised version was published online in June 2006 with corrections to the Cover Date.     

Chlorophyll breakdown in spinach: on the structure of five nonfluorescent chlorophyll catabolites*

In extracts of senescent leaves of spinach (Spinacia oleracea), five colourless compounds with UV/Vis-characteristics of nonfluorescent chlorophyll catabolites (NCCs) were detected and tentatively named So-NCCs. The most abundant polar NCC in the leaves of this vegetable, So-NCC-2, had been isolated earlier and its constitution was determined by spectroscopic means. The catabolite So-NCC-2 was found to be an epimer of a polar NCC from barley (Hordeum vulgare), the first non-green chlorophyll catabolite from a higher plant to be structurally analyzed. Here, we report on the isolation of four additional So-NCCs from the extracts of senescent leaves of Sp. oleracea by two- (or multi-)stage chromatographic purification and on their structural characterization. The constitution of So-NCC-3 could be determined by spectroscopic analysis in combination with chemical correlation with a known NCC from Cercidiphyllum japonicum (Cj-NCC): So-NCC-3 was identified as the hydrolysis product of the methyl ester function of Cj-NCC. The less polar catabolite So-NCC-4 could be directly identified with Cj-NCC. Two further So-NCCs, So-NCC-1 and So-NCC-5, were detected only in trace amounts. Five structurally related nonfluorescent chlorophyll catabolites (So-NCCs) are thus present in senescent leaves of spinach. The structures of this set of So-NCCs indicate several peripheral refunctionalization reactions and inform on the late catabolic transformations during leaf senescence. The transformation of the tetrapyrrolic skeleton in chlorophyll catabolism in spinach and in C. japonicum is revealed to exhibit a common stereochemical pattern. This revised version was published online in June 2006 with corrections to the Cover Date.     

Recent advances in the role and biosynthesis of ascorbic acid in plants

The past few years have provided many advances in the role and biosynthesis of L -ascorbic acid (AsA) in plants. There is an increasing body of evidence confirming that AsA plays an important role in the detoxification of reactive oxygen species. The role of AsA in photoprotection has been confirmed in vivo with the use of Arabidopsis mutants. A player in the defence against reactive oxygen species, AsA peroxidase, has been extensively studied at the molecular level, and regulation of this key enzymatic activity appears to occur at several levels. As a cofactor in the hydroxylation of prolyl and lysl-residues by peptidyl-prolyl and -lysyl hydroxylases, AsA plays a part in cell wall synthesis, defence, and possibly cell division. The maintenance of reduced levels of AsA appears to be highly regulated, involving the interplay of both monodehydroascorbate and dehydroascorbate reductases and possibly auxin. A major breakthrough in plant AsA biosynthesis has been made recently, and strong biochemical and genetic evidence suggest that GDP-mannose and L -galactose are key substrates. In addition, evidence for an alternative AsA biosynthetic pathway(s) exists and awaits additional scrutiny. Finally, newly described Arabidopsis mutants deficient in AsA will further increase our understanding of AsA biosynthesis     

Small Cab-like proteins regulating tetrapyrrole biosynthesis in the cyanobacterium Synechocystis sp. PCC 6803

In the cyanobacterium Synechocystis sp. PCC 6803 five open reading frames (scpA–scpE) have been identified that code for single-helix proteins resembling helices I and III of chlorophyll a/b-binding (Cab) antenna proteins from higher plants. They have been named SCPs (small Cab-like proteins). Deletion of a single scp gene in a wild-type or in a photosystem I-less (PS I-less) strain has little effect. However, the effects of functional deletion of scpB or scpE were remarkable under conditions where chlorophyll availability was limited. When cells of a strain lacking PS I and chlL (coding for a polypeptide needed for light-independent protochlorophyllide reduction) were grown in darkness, the phycobilin and protochlorophyllide levels decreased upon deletion of scpB or scpE and the protoheme level was reduced in the strain lacking scpE. Addition of -aminolevulinic acid (ALA) in darkness drastically increased the level of Mg-protoporphyrin IX and Mg-protoporphyrin IX monomethyl ester in the PS I-less/chlL ^–/scpE ^– strain, whereas PChlide accumulated in the PS I-less/chlL ^–/scpB ^– strain. In the PS I-less/chlL ^– control strain ALA supplementation did not lead to large changes in the levels of tetrapyrrole biosynthesis intermediates. We propose that ScpE and ScpB regulate tetrapyrrole biosynthesis as a function of pigment availability. This regulation occurs primarily at an early step of tetrapyrrole biosynthesis, prior to ALA. In view of the conserved nature of chlorophyll-binding sites in these proteins, it seems likely that regulation by SCPs occurs as a function of chlorophyll availability, with SCPs activating chlorophyll biosynthesis steps when they do not have pigments bound.     

A gene cluster inChlorobium vibrioforme encoding the first enzymes of chlorophyll biosynthesis

A cloned 5.8-kb genomic fragment of the green sulfur bacteriumChlorobium vibrioforme encodes the genes for three enzymes catalyzing early steps in the biosynthetic pathway of tetrapyrroles, common to chlorophyll and heme. ThehemA, hemC andhemD genes encode the enzymes glutamyl tRNA dehydrogenase, porphobilinogen deaminase and uroporphyrinogen III synthase, respectively. The cloned genes were expressed in transformedEscherichia coli orSalmonella typhimurium and conferred autotrophy on the respective auxotrophs. Activities of the enzymes encoded by the cloned genes were demonstrated in vitro, with cell extracts obtained from the transformed enterobacteria. The proximity of these genes indicates that they form a cluster inChlorobium vibrioforme, while in most other organisms they appear to be scattered. The presence of this cluster may imply coordinate regulation of the genes involved and they may constitute an operon.     

Abscisic acid physiology and biosynthesis in higher plants

Abscisic acid (ABA) has been postulated to modulate several aspects of plant growth and development. While it is tempting to attribute changes in growth and development to a specific hormone such as ABA, the reality is that these processes are complex and poorly understood. Since there is so little known about basic biochemical events that occur during growth and development, it is difficult ot unambiguously assign a role for ABA in any process. Becuse of this, many of the cited effects of ABA on growth and development have not been conclusively demonstrated. Howver, it is clear that ABA has a function in ameliorating water-stress and preventing vivipary. The roles of ABA in bud dormancy and growth still remain unclear. With the use of biosynthesis inhibitors and mutants which block ABA accumulation, it has been shown that ABA does not play a role in gravitropism.
Knowledge of how the levels of any particular growth regulator are modulated is essential for the understanding of its physiology. The use of mutants, inhibitors and heavy isotopes suggests that ABA may be derived from a carotenoid rather than directly from farnesyl pyrophosphate (FPP), and that the cleavage of a carotenoid is the rate limiting step. However, the relative contribution of each pathway (and the role of xanthoxin) in ABA biosynthesis remain unknown.     

The role of a long-wavelength pigment form in the chlorophyll biosynthesis

Photoconversion of protochlorophyllide₆₅₀ form was observed in etiolated leaves illuminated with long-wavelength—690 nm—light. This process showed Shibata shift and was found to have a strong temperature dependence between 20 and –40°C. The low rate of reaction, the strong temperature dependence and calculations on the spectral overlap integral of absorption and fluorescence bands in this spectral region indicate that the phototransformation of the 650 nm form of protochlorophyllide may be caused by a back energy migration from a long-wavelength pigment form absorbing around 690 nm; this pigment form is probably a long-wavelength form of protochlorophyll/ide.     

Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis

Protoporphyrinogen IX oxidase (PPO), the last common enzyme of haem and chlorophyll biosynthesis, catalyses the oxidation of protoporphyrinogen IX to protoporphyrin IX. The membrane-embedded flavoprotein is the target of a large class of herbicides. In humans, a defect in PPO is responsible for the dominantly inherited disease variegate porphyria. Here we present the crystal structure of mitochondrial PPO from tobacco complexed with a phenyl-pyrazol inhibitor. PPO forms a loosely associated dimer and folds into an FAD-binding domain of the p-hydroxybenzoate-hydrolase fold and a substrate-binding domain that enclose a narrow active site cavity beneath the FAD and an alpha-helical membrane-binding domain. The active site architecture suggests a specific substrate-binding mode compatible with the unusual six-electron oxidation. The membrane-binding domains can be docked onto the dimeric structure of human ferrochelatase, the next enzyme in haem biosynthesis, embedded in the opposite side of the membrane. This modelled transmembrane complex provides a structural explanation for the uncoupling of haem biosynthesis observed in variegate porphyria patients and in plants after inhibiting PPO.     

A new pathway of chlorophyll biosynthesis from long-wavelength protochlorophyllide Pchlide 686/676 in juvenile etiolated plants

By spectral methods, the final stages of chlorophyll formation from protochlorophyllide were studied using etiolated pea, bean, barley, wheat and maize plants in early stages (4 days) of growth. For these juvenile plants, along with the reaction chain known for mature (7–9-day-old) plants, a new reaction chain was found, which started with phototransformation of the long-wavelength form Pchlide 686/676(440) into Pchlide 653/648(440). (Pchlide 653/648(440) differs from the main known precursor form Pchlide 655/650(448)). The subsequent photoreduction of Pchlide 653/648(440) leads to the formation of Chlide 684/676(440), which is transformed into Chl 688/680(440) in the course of a dark reaction. After completion of this reaction, fast (20–30 s) quenching of the low-temperature fluorescence of the reaction product is observed with the formation of non-fluorescent Chl 680. The reaction accompanied by pigment fluorescence quenching is absent in pea mutants with depressed function of Photosystem II reaction centers. This suggests that the newly found reaction chain leads to the formation of chlorophyll of the Photosystem II core. This revised version was published online in June 2006 with corrections to the Cover Date.     

The <Emphasis Type="Italic">Chlamydomonas reinhardtii gtr </Emphasis>Gene Encoding the Tetrapyrrole Biosynthetic Enzyme Glutamyl-tRNA Reductase: Structure of the Gene and Properties of the Expressed Enzyme

Plants, algae, cyanobacteria and many other bacteria synthesize the tetrapyrrole precursor, δ-aminolevulinic acid (ALA), from glutamate by means of a tRNA^Glu-mediated pathway. The enzyme glutamyl-tRNA reductase (GTR) catalyzes the first committed step in this pathway, which is the reduction of tRNA-bound glutamate to produce glutamate 1-semialdehyde. Chlamydomonas reinhardtii mRNA encoding gtr was sequenced from a cDNA and genomic libraries. The 3179-bp gtr cDNA contains a 1566-bp open reading frame that encodes a 522-amino acid polypeptide. After removal of the predicted transit peptide, the mature 480-residue GTR has a calculated molecular weight of 52,502. The deduced C. reinhardtii mature GTR amino acid sequence has more than 55% identity to a GTR sequence of Arabidopsis thaliana, and significant similarity to GTR proteins of other plants and prokaryotes. Southern blot analysis of C. reinhardtii genomic DNA indicates that C. reinhardtii has only one gtr gene. Genomic DNA sequencing revealed the presence of a small intron near the putative transit peptide cleavage site. Expression constructs for the full-length initial gtr translation product, the mature protein after transit peptide removal, and the coding sequence of the second exon were cloned into expression vector that also introduced a C-terminal His₆ tag. All of these constructs were expressed in E. coli, and both the mature protein and the exon 2 translation product complemented a hemA mutation. The expressed proteins were purified by Ni-affinity column chromatography to yield active GTR. Purified mature GTR was not inhibited by heme, but heme inhibition was restored upon addition of C. reinhardtii soluble proteins.     

Incorporation of 5-aminolevulinic acid into chlorophyll in darkness in barley

The incorporation of radioactive aminolevulinic acid (ALA) into chlorophyll (Chl) a and b , as well as protochlorophyllide (Pchlide) in light-grown barley seedlings ( Hordeum vulgare L. cv. Clipper) transferred to darkness is demonstrated.
In the experiments described, 6-day-old, glasshouse-grown seedlings were transferred to darkness and incubated in [¹⁴C]- or [³H]- ALA for 18 h.
Chl a and b were extracted and purified to constant specific radioactivity by HPLC and TLC of their magnesium-free derivatives, pheophytin a and b . The presence of label in the tetrapyrrole ring of the Chls was established by removal of the phytol chain by alkaline hydrolysis and determination of the specific radioactivity of the chlorin e ₆ and rhodin g ₇ derivatives.
Barley seedlings that had been grown in darkness for 5 days, transferred to light for 20 h, and then returned to darkness in the presence of radioactive ALA also incorporated label into Chl. However, this was only apparent in intact seedlings. Excised leaves from greened etiolated plants did not incorporate ALA into Chl in darkness. This was consistent with the finding of Apel et al. (K. Apel, M. Motzkus and K. Dehesh, 1984. Planta 161: 550–554) and may account for their failure to obtain evidence for a light-independent protochlorophyllide reductase in greening barley.
Although the incorporation of ALA into Chl compared to Pchlide was slight (5%), the presence of label in the tetrapyrrole nucleus of Chl a and b is unequivocal evidence of a light-independent pathway of Chl biosynthesis in barley that has been exposed to light during development. Limited entry of exogenous labelled ALA into the precursor pools leading to the dark reduction of Pchlide is postulated.     

Pantothenate biosynthesis in higher plants: advances and challenges

Pantothenate (vitamin B₅) is the precursor of the 4'-phosphopantetheine moiety of coenzyme A and acyl-carrier protein. Plants and microorganisms make the vitamin de novo, whereas animals must obtain it from their diet. Pantothenate is produced commercially by chemical synthesis for vitamin supplements, feed additives and cosmetics. An attractive alternative for production is biotransformation, which would avoid expensive procedures for separation of racemic intermediates. The biosynthetic pathway in bacteria, comprising four enzymic reactions, is well-established, and enzymes from Escherichia coli have been fully characterized including the overexpression and purification of recombinant enzymes and the determination of their X-ray crystal structures. Pantothenate biosynthesis in higher plants is beginning to be elucidated, and genes encoding the first and last enzymes have been identified and characterized in Arabidopsis thaliana and Oryza sativa (rice). This review describes our current understanding of the pathway in plants and the challenges that lie ahead in engineering plants to make increased amounts of the vitamin.     

Controlling the delicate balance of tetrapyrrole biosynthesis

Tetrapyrroles are a family of compounds that contain four pyrrole rings. They are involved in many fundamental biological processes such as photoreception, electron transport, gas transport and also as cofactors for enzymatic reactions. As regulators of protein activity, tetrapyrroles mediate cellular response to light, oxygen and nutrient levels in the surrounding environment. Biosynthesis of haem tetrapyrroles shares, conserved pathways and enzymes among all three domains of life. This is contrasted by chlorophyll biosynthesis that is only present in eubacteria and chloroplasts, or cobalamin biosynthesis that is only present in eubacteria and archaea. This implicates haem as the most ancient, and chlorophyll as the most recent, of the common tetrapyrroles that are currently synthesized by existing organisms. Haem and chlorophyll are both toxic when synthesized in excess over apo-proteins that bind these tetrapyrroles. Accordingly, the synthesis of these tetrapyrroles has to be tightly regulated and coordinated with apo-protein production. The mechanism of regulating haem and chlorophyll synthesis has been studied intensively in Rhodobacter species and will be discussed.     

Yellow lupin cytoplasmic tRNAGlu is not a cofactor in chlorophyll biosynthesis

Yellow lupin seeds (Lupinus luteus) cytoplasmic tRNA^Glu was isolated and the primary structure was determined to be: pUCCGUUGUAGUCAGDDGGDCAGGAUAUUCGGCUCUCACCCGAAAGACm⁵CCGGGTCAm¹ AGU CCCGGCGACGGAACCA_OH. It is 76 nucleotides long and contains 8 modified nucleosides: 2 residues of pseudouridine, ribothymidine, 3 dihydrouridines, 5-methylcytosine and 1-methyladenosine. This tRNA^Glu assayed in -aminolevulinic acid synthesis was shown to be inactive. Its structural festures are discussed.