Higher Plant Chloroplasts Research Articles

Cytoenzymological analysis of adenylyl cyclase activity and 3′:5′‐cAMP immunolocalization in chloroplasts of Nicotiana tabacum

In this study a combination of cytoenzymological and immunocytochemical techniques was used in order to demonstrate the presence of cyclic nucleotide metabolism in chloroplasts of higher plants. Catalytic cytochemistry was used to localize adenylyl cyclase activity by means of electron microscope investigation on Nicotiana tabacum cv. Petit Havana leaf fragments. Various immunocytochemical techniques were explored to visualize the presence of the second messenger adenosine 3':5'-cyclic monophosphate. Making use of adenylyl imidodiphosphate as a substrate, the enzyme activity was predominantly located at the intermembrane space of the chloroplast envelope. In order to provide further topographical information, intact, isolated chloroplasts were submitted to the same cytoenzymological procedure and revealed stromal adenylyl cyclase activity. Using high-pressure freezing as a physical fixative to obtain an instantaneous metabolic arrest the cellular vitrified water phase was sublimed under ultra-high vacuum by means of molecular distillation drying, avoiding recrystallization and hence redistribution of small highly diffusible molecules. This sequential combination preserved 3':5'-cAMP epitope retention in chloroplasts as was demonstrated by immunogold labelling. These results further substantiate in a unique way the growing evidence of the presence of an organelle-specific cAMP metabolism in higher plants. Furthermore the data presented support the status of chloroplasts as an excellent model to further investigate cAMP metabolism and to correlate it with a variety of physiological functions.

A decade of progress in understanding vitamin E synthesis in plants

The chloroplasts of higher plants contain and elaborate many unique biochemical pathways that produce an astonishing array of compounds that are vital for plastid function and are also important from agricultural and nutritional perspectives. One such group of compounds is the tocochromanols (more commonly known as Vitamin E), which is a class of four tocopherols and four toctorienols, lipid-soluble antioxidants that are only synthesized by plants and other oxygenic, photosynthetic organisms. Though the essential nature of tocopherols in mammalian diets was recognized over 80 years ago and the biosynthetic pathway in plants and algae elucidated in the late 1970s and early 80s, it has only been in the past decade that the genes and proteins for tocopherol synthesis have finally been isolated and characterized. The use of model plant and cyanobacterial systems has driven this gene discovery to the point that manipulation of tocopherol levels and types in various plant tissues and crops is becoming a reality. This article reviews progress since 1996 in the molecular and genetic understanding of tocopherol synthesis in the model photosynthetic organisms Arabidopsis thaliana and Synechocystis PCC6803 as a primer for current and future efforts to manipulate the levels of this essential nutrient in food crops by breeding and transgenic approaches.

The ATP‐dependent Clp protease in chloroplasts of higher plants

The best‐known proteases in plastids are those that belong to families common to eubacteria. One of the first identified was the ATP‐dependent caseinolytic protease (Clp), whose structure and function have been well characterized in Escherichia coli. Plastid Clp proteins in higher plants are surprisingly numerous and diverse, with at least 16 distinct Clp proteins in the model plant Arabidopsis thaliana. Multiple paralogues exist for several of the different types of plastid Clp protein, with the most extreme being five for the proteolytic subunit ClpP. Both biochemical and genetic studies have recently begun to reveal the intricate structural interactions between the various Clp proteins, and their importance for chloroplast function and plant development. Much of the recent data suggests that the function of many of the Clp proteins probably affects more specific processes within chloroplasts, in addition to the more general ‘housekeeping’ role previously assumed.

The family of Deg proteases in cyanobacteria and chloroplasts of higher plants

The family of Deg proteases is present in nearly all organisms from bacteria to higher plants. This family consists of ATP‐independent serine endopeptidases with a catalytic domain of trypsin type and up to three PDZ domains, involved in protein–protein interactions. Sixteen deg genes (originally named degP1–16) were found in Arabidopsis thaliana, and the chloroplast location was predicted or experimentally proven for seven proteins. The cyanobacterium Synechocystis sp. PCC6803 contains three Deg homologues, HtrA (DegP), HhoA (DegQ) and HhoB (DegS), but their number can vary between one and six in other photosynthetic Prokaryota. Interestingly, all of these proteases are evolutionarily more closely related within one species than proteases with the same names present in other organisms. This means that Deg proteases from A. thaliana are not necessarily the closest relatives of cyanobacterial DegP. Therefore, we propose to change the misleading original name ‘DegP’ to ‘Deg’ for A. thaliana enzymes. Here, we summarize the expression, location and functions of Deg proteases from cyanobacteria and chloroplasts of higher plants, with special emphasis on their role in the photosystem II (PSII) repair cycle under light stress conditions.

A conserved inverted repeat from rice plastome functions as an intrinsic transcription terminator

Results from a previous rice transcription mapping and the GeSTer algorithm analysis used in this in-vestigation for rice plastid genome suggest that an inverted repeat, IRsl8, in 3′ region of the plastid rps18 gene may serve as a transcription terminator. The in vitro transcription assay showed that the transcript ending at the IRsl8 was not proc-essed by ribonucleases but terminated intrinsically in an rNTP substrate-dependent manner as demonstrated for the first time in plant gene regulation. For the poly-T tract (TTCTTTTTT) 3′-proximal to the IRsl8, the C base conver-sion to T resulting in a perfect 9 Ts can dramatically increase termination efficiency, which is a common feature of bacte-rial intrinsic termination. This study is the first case to indi-cate that a conserved inverted repeat with a poly-T tract from higher plant chloroplast contributes to transcription termination of the translation-associated rps18 gene in a manner with the intrinsic termination, probably resulting from a heritage of endosymbiosis.

Blue light-induced orientation movements of chloroplasts in higher plants: Recent progress in the study of their mechanisms

The discovery of phototropins, photoreceptors for chloroplast responses in Arabidopsis thaliana, brought about renewed interest in these blue light-controlled movements. Recent progress in research on their mechanisms in higher plants is briefly summarized. Phototropins mediate phototropism, chloroplast relocations and stomatal movements. Their functions are partially overlapping, with phot1 active predominantly in weak light and phot2 active in strong light. The accumulation response of chloroplasts appears to be mediated by phot1 and phot2 whereas the avoidance response is controlled by phot2. The role of Ca2+ as a potential intracellular messenger has been discussed in view of the recently demonstrated blue light-induced transient increases in the cytosolic Ca2+ mediated differently by phot1 and phot2. Differential inhibition of accumulation and avoidance responses by wortmannin, the inhibitor of phosphoinositide-3 kinases, in Lemna trisulca points to an important role of these enzymes in the signal transduction. A new, multi-domain component controlling chloroplast positioning and movement, CHUP1, encodes an actin-binding protein in Arabidopsis.

Identification of Chloroplast Signal Recognition Particle RNA Genes

The signal recognition particle (SRP) is a ribonucleoprotein complex responsible for targeting proteins to the ER membrane in eukaryotes, the plasma membrane in bacteria and the thylakoid membrane in chloroplasts. In higher plants two different SRP-dependent mechanisms have been identified: one post-translational for proteins imported to the chloroplast and one co-translational for proteins encoded by the plastid genome. The post-translational chloroplast SRP (cpSRP) consists of the protein subunits cpSRP54 and cpSRP43. An RNA component has not been identified and does not seem to be required for the post-translational cpSRP. The co-translational mechanism is known to involve cpSRP54, but an RNA component has not yet been identified. Several chloroplast genomes have been sequenced recently, making a phylogenetically broad computational search for cpSRP RNA possible. We have analysed chloroplast genomes from 27 organisms. In higher plant chloroplasts, no SRP RNA genes were identified. However, eight plastids from red algae and Chlorophyta were found to contain an SRP RNA gene. These results suggest that SRP RNA forms a complex in these plastids with cpSRP54, reminiscent of the eubacterial SRP.

High light stress inducing photoinhibition and protein degradation of photosystem I in Brassica rapa

PSI is one of the two photosynthetic reaction centers in the chloroplast of higher plants. It functions as a plastocyanin:ferredoxin oxidoreductase that catalyzes light-dependent electron transfer from reduced plastocyanin to oxidized ferredoxin. In order to understand the functional flexibility (i.e. stability, turnover and adaptation to stress) of PSI, a series of light stress conditions were introduced to induce PSI photoinhibition in Brassica rapa plants. Thylakoid membranes were subsequently isolated, and PSI photochemical activity and protein degradation were examined. The results demonstrated that high light stress (600 μmol photon m −2 s −1 versus 100 μmol photon m −2 s −1) induced PSI photoinhibition, by up to 35% decrease of PSI activity within 2–4 h. In addition, we found a recovery response of PSI to the high light stress, which brought the decreased PSI activity to a much higher level within 20–24 h, equivalent to that grown in constant high light conditions. However, this recovery process of PSI was eliminated and more severe PSI photoinhibition was induced by a combination of high light with drought and/or high temperature (35 °C). Western blotting analysis further showed that light-induced reduction of PSI activity was concomitant with degradation of PsaA and PsaB, and loss of PsaC in the thylakoid membranes. These results indicate that PSI photoinhibition may occur in most crop plants in a growth season since its reaction center proteins are the very early targets of photooxidative stresses.

In vitro RNA editing systems from higher plant chloroplasts.

RNA editing in higher plant chloroplasts involves C-to-U conversion at ~30 specific sites. In vitro systems supporting accurate editing have been developed from tobacco and pea chloroplasts. mRNA substrates labeled with 32P at C residues to be edited provide sensitive detection of editing activity in vitro. The present systems allow the rapid identification of cis-elements using mutated mRNA substrates and trans-acting factors by ultraviolet crosslinking.

Studying RNA editing in transgenic chloroplasts of higher plants.

RNA editing in plant cell organelles is a posttranscriptional process that changes the identity of individual nucleotides by pyrimidine transitions. C-to-U conversions are the predominantly found modifications in both mitochondrial and chloroplast transcripts of vascular plants. Research on functional, mechanistic, and evolutionary aspects of plant RNA editing has benefited immensely from the development of transgenic technologies for higher plant chloroplasts. This chapter describes methods for the generation of plants with stably transformed chloroplast genomes and their use for studying RNA editing processes in vivo.

A site-specific factor interacts directly with its cognate RNA editing site in chloroplast transcripts.

RNA editing involves a variety of genetic systems and occurs by different mechanisms. In higher plant chloroplasts, specific sites of some transcripts are subject to C-to-U conversion. We have previously shown that site-specific trans-acting factors for psbE and petB mRNA editing bind corresponding cis-elements, which are located 5 nucleotides upstream from the editing site. Here we report that, by using mRNAs labeled either at the center of the upstream cis-element or at the editing site, the site-specific factors can be cross-linked with nucleotides at both positions. Mutations of nucleotides in the proximal region of the editing site revealed a correlation between editing activity and cross-linking efficiency of factors with the editing site, even though cross-linking with the upstream cis-element was unaffected. These observations suggest that the site-specific factor binds stably to the upstream ciselement, whereas it interacts weakly with the editing site. This finding raises the intriguing possibility that the site-specific factor is involved in both site-determination and C-to-U conversion in chloroplast RNA editing.

Tracking the function of the cytochrome c6-like protein in higher plants

The contention that plastocyanin is the only mobile electron donor to photosystem I in higher plants was recently shaken by the discovery of a cytochrome c 6-like protein in Arabidopsis and other flowering plants. However, the genetic and biochemical data presented in support of the idea that the cytochrome c 6 homologue can replace plastocyanin have now been challenged by two complementary studies. This re-opens the debate on the real function(s) of cytochrome c in the chloroplasts of higher plants.

Manipulating ribulose bisphosphate carboxylase/oxygenase in the chloroplasts of higher plants

Transgenic manipulation of the photosynthetic CO 2-fixing enzyme, ribulose bisphosphate carboxylase/oxygenase (Rubisco) in higher plants provides a very specific means of testing theories about photosynthesis and its regulation. It also encourages prospects for radically improving the efficiencies with which photosynthesis and plants use the basic resources of light, water, and nutrients. Manipulation was once limited to variation of the leaf’s total content of Rubisco by transforming the nucleus with antisense genes directed at the small subunit. More recently, technology for transforming the small genome of the plastid of tobacco has enabled much more precise manipulation and replacement of the plastome-encoded large subunit. Engineered changes in Rubisco’s properties in vivo are reflected as profound changes in the photosynthetic gas-exchange properties of the leaves and the growth requirements of the plants. Unpredictable expression of plastid transgenes and assembly requirements of some foreign Rubiscos that are not satisfied in higher-plant plastids provide challenges for future research.

PNPase activity determines the efficiency of mRNA 3'-end processing, the degradation of tRNA and the extent of polyadenylation in chloroplasts.

The exoribonuclease polynucleotide phosphorylase (PNPase) has been implicated in mRNA processing and degradation in bacteria as well as in chloroplasts of higher plants. Here, we report the first comprehensive in vivo study of chloroplast PNPase function. Modulation of PNPase activity in Arabidopsis chloroplasts by a reverse genetic approach revealed that, although this enzyme is essential for efficient 3'-end processing of mRNAs, it is insufficient to mediate transcript degradation. Surprisingly, we identified PNPase as also being indispensable for 3'-end maturation of 23S rRNA transcripts. Analysis of tRNA amounts in transgenic Arabidopsis plants suggests a direct correlation of PNPase activity and tRNA levels, indicating an additional function of this exoribo nuclease in tRNA decay. Moreover, the extent of polyadenylated mRNAs in chloroplasts is negatively correlated with PNPase activity. Together, our results attribute novel functions to PNPase in the metabolism of all major classes of plastid RNAs and suggest an unexpectedly complex role for PNPase in RNA processing and decay.

Co-existence of two regulatory NADP-glyceraldehyde 3-P dehydrogenase complexes in higher plant chloroplasts.

Light/dark modulation of the higher plant Calvin-cycle enzymes phosphoribulokinase (PRK) and NADP-dependent glyceraldehyde 3-phosphate dehydrogenase (NADP- GAPDH-A2B2) involves changes of their aggregation state in addition to redox changes of regulatory cysteines. Here we demonstrate that plants possess two different complexes containing the inactive forms (a) of NADP-GAPDH and PRK and (b) of only NADP-GAPDH, respectively, in darkened chloroplasts. While the 550-kDa PRK/GAPDH/CP12 complex is dissociated and activated upon reduction alone, activation and dissociation of the 600-kDa A8B8 complex of NADP-GAPDH requires incubation with dithiothreitol and the effector 1,3-bisphosphoglycerate. In the light, PRK is therefore completely in its activated state under all conditions, even in low light, while GAPDH activation in the light is characterized by a two-step mechanism with 60-70% activation under most conditions in the light, and the activation of the remaining 30-40% occurring only when 1,3-bisphosphoglycerate levels are strongly increasing. In vitro studies with the purified components and coprecipitation experiments from fresh stroma using polyclonal antisera confirm the existence of these two aggregates. Isolated oxidized PRK alone does not reaggregate after it has been purified in its reduced form; only in the presence of both CP12 and purified NADP-GAPDH, some of the PRK reaggregates. Recombinant GapA/GapB constructs form the A8B8 complex immediately upon expression in E. coli.

Recognition of RNA editing sites is directed by unique proteins in chloroplasts: biochemical identification of cis-acting elements and trans-acting factors involved in RNA editing in tobacco and pea chloroplasts.

RNA editing in higher-plant chloroplasts involves C-to-U conversions at specific sites. Although in vivo analyses have been performed, little is known about the biochemical aspects of chloroplast editing reactions. Here we improved our original in vitro system and devised a procedure for preparing active chloroplast extracts not only from tobacco plants but also from pea plants. Using our tobacco in vitro system, cis-acting elements were defined for psbE and petB mRNAs. Distinct proteins were found to bind specifically to each cis-element, a 56-kDa protein to the psbE site and a 70-kDa species to the petB site. Pea chloroplasts lack the corresponding editing site in psbE since T is already present in the DNA. Parallel in vitro analyses with tobacco and pea extracts revealed that the pea plant has no editing activity for psbE mRNAs and lacks the 56-kDa protein, whereas petB mRNAs are edited and the 70-kDa protein is also present. Therefore, coevolution of an editing site and its cognate trans-factor was demonstrated biochemically in psbE mRNA editing between tobacco and pea plants.

Involvement of a Plastid Terminal Oxidase in Plastoquinone Oxidation as Evidenced by Expression of the Arabidopsis thaliana Enzyme in Tobacco

Chlororespiration has been defined as a respiratory electron transport chain in interaction with photosynthetic electron transport involving both non-photochemical reduction and oxidation of plastoquinones. Different enzymatic activities, including a plastid-encoded NADH dehydrogenase complex, have been reported to be involved in the non-photochemical reduction of plastoquinones. However, the enzyme responsible for plasquinol oxidation has not yet been clearly identified. In order to determine whether the newly discovered plastid oxidase (PTOX) involved in carotenoid biosynthesis acts as a plastoquinol oxidase in higher plant chloroplasts, the Arabidopsis thaliana PTOX gene (At-PTOX) was expressed in tobacco under the control of a strong constitutive promoter. We showed that At-PTOX is functional in tobacco chloroplasts and strongly accelerates the non-photochemical reoxidation of plastoquinols; this effect was inhibited by propyl gallate, a known inhibitor of PTOX. During the dark to light induction phase of photosynthesis at low irradiances, At-PTOX drives significant electron flow to O(2), thus avoiding over-reduction of plastoquinones, when photo- synthetic CO(2) assimilation was not fully induced. We proposed that PTOX, by modulating the redox state of intersystem electron carriers, may participate in the regulation of cyclic electron flow around photosystem I.

Chlororespiration.

Chlororespiration has been defined as a respiratory electron transport chain (ETC) in interaction with the photosynthetic ETC in thylakoid membranes of chloroplasts. The existence of chlororespiration has been disputed during the last decade, with the initial evidence mainly obtained with intact algal cells being possibly explained by redox interactions between chloroplasts and mitochondria. The discovery in higher-plant chloroplasts of a plastid-encoded NAD(P)H-dehydrogenase (Ndh) complex, homologous to the bacterial complex I, and of a nuclear-encoded plastid terminal oxidase (PTOX), homologous to the plant mitochondrial alternative oxidase, brought molecular support to the concept of chlororespiration. The functionality of these proteins in non-photochemical reduction and oxidation of plastoquinones (PQs), respectively, has recently been demonstrated. In thylakoids of mature chloroplasts, chlororespiration appears to be a relatively minor pathway compared to linear photosynthetic electron flow from H2O to NADP+. However, chlororespiration might play a role in the regulation of photosynthesis by modulating the activity of cyclic electron flow around photosystem I (PS I). In non-photosynthetic plastids, chlororespiratory electron carriers are more abundant and may play a significant bioenergetic role.

Regulation and function of ascorbate peroxidase isoenzymes

Even under optimal conditions, many metabolic processes, including the chloroplastic, mitochondrial, and plasma membrane-linked electron transport systems of higher plants, produce active oxygen species (AOS). Furthermore, the imposition of biotic and abiotic stress conditions can give rise to excess concentrations of AOS, resulting in oxidative damage at the cellular level. Therefore, antioxidants and antioxidant enzymes function to interrupt the cascades of uncontrolled oxidation in each organelle. Ascorbate peroxidase (APX) exists as isoenzymes and plays an important role in the metabolism of H(2)O(2) in higher plants. APX is also found in eukaryotic algae. The characterization of APX isoenzymes and the sequence analysis of their clones have led to a number of investigations that have yielded interesting and novel information on these enzymes. Interestingly, APX isoenzymes of chloroplasts in higher plants are encoded by only one gene, and their mRNAs are generated by alternative splicing of the gene's two 3'-terminal exons. Manipulation of the expression of the enzymes involved in the AOS-scavenging systems by gene-transfer technology has provided a powerful tool for increasing the present understanding of the potential of the defence network against oxidative damage caused by environmental stresses. Transgenic plants expressing E. coli catalase to chloroplasts with increased tolerance to oxidative stress indicate that AOS-scavenging enzymes, especially chloroplastic APX isoenzymes are sensitive under oxidative stress conditions. It is clear that a high level of endogenous ascorbate is essential effectively to maintain the antioxidant system that protects plants from oxidative damage due to biotic and abiotic stresses.

Regulation and function of ascorbate peroxidase isoenzymes

Even under optimal conditions, many metabolic processes, including the chloroplastic, mitochondrial, and plasma membrane‐linked electron transport systems of higher plants, produce active oxygen species (AOS). Furthermore, the imposition of biotic and abiotic stress conditions can give rise to excess concentrations of AOS, resulting in oxidative damage at the cellular level. Therefore, antioxidants and antioxidant enzymes function to interrupt the cascades of uncontrolled oxidation in each organelle. Ascorbate peroxidase (APX) exists as isoenzymes and plays an important role in the metabolism of H2O2 in higher plants. APX is also found in eukaryotic algae. The characterization of APX isoenzymes and the sequence analysis of their clones have led to a number of investigations that have yielded interesting and novel information on these enzymes. Interestingly, APX isoenzymes of chloroplasts in higher plants are encoded by only one gene, and their mRNAs are generated by alternative splicing of the gene's two 3′‐terminal exons. Manipulation of the expression of the enzymes involved in the AOS‐scavenging systems by gene‐transfer technology has provided a powerful tool for increasing the present understanding of the potential of the defence network against oxidative damage caused by environmental stresses. Transgenic plants expressing E. coli catalase to chloroplasts with increased tolerance to oxidative stress indicate that AOS‐scavenging enzymes, especially chloroplastic APX isoenzymes are sensitive under oxidative stress conditions. It is clear that a high level of endogenous ascorbate is essential effectively to maintain the antioxidant system that protects plants from oxidative damage due to biotic and abiotic stresses.