植物Rubisco活性中心的模拟分析

通过对与不同配基结合的植物Rubisco复合物结构的重叠比较分析 ,发现Rubisco的活性差异是由其中一段Loop6环序列所造成的 ;金属离子与活性中心的结合会造成活性中心巨大的构象变化 .进一步用SwissPDBViewer软件模拟不同配基的植物Rubisco活性中心与此Loop环的氢键相互作用 .结果表明 ,有 3个Lys残基Lys2 0 1、Lys334、Lys175与Rubisco是否处于活性状态密切相关 ,这些残基的结构变化对分子设计可能有重要的参考价值     

Changes in photosynthetic apparatus of mustard (<Emphasis Type="Italic">Sinapis alba</Emphasis>) cotyledons following cycloheximide and kinetin treatments

Biochemical and accompanying structural characteristics of the photosynthetic process were studied in mustard seedlings cultivated on medium with increasing concentrations of cycloheximide alone as well as in combination with various kinetin concentrations. After 7 days of cultivation the contents of total chlorophyll, carotenoids and content of Rubisco in mustard cotyledons were determined. The content of chlorophyll pigments and carotenoids decreased in dependence of cycloheximide concentration. Following antibiotic treatment the content of both Rubisco subunits markedly decreased. In addition cycloheximide caused disturbance in mesophyll organization and chloroplast ultrastructure. Kinetin applied with cycloheximide increased the amount of photosynthetic pigments as well as of Rubisco, compared to the cycloheximide alone. In the seedlings treated with cycloheximide+kinetin the structure of leaf mesophyll and chloroplast membrane system was similar to control. Our results indicate that kinetin diminished the negative effects of cycloheximide on photosynthetic pigments and Rubisco as well as on the structural traits of the cotyledons.     

NOA1 functions in a temperature-dependent manner to regulate chlorophyll biosynthesis and Rubisco formation in rice

NITRIC OXIDE-ASSOCIATED1 (NOA1) encodes a circularly permuted GTPase (cGTPase) known to be essential for ribosome assembly in plants. While the reduced chlorophyll and Rubisco phenotypes were formerly noticed in both NOA1-suppressed rice and Arabidopsis, a detailed insight is still necessary. In this study, by using RNAi transgenic rice, we further demonstrate that NOA1 functions in a temperature-dependent manner to regulate chlorophyll and Rubisco levels. When plants were grown at 30°C, the chlorophyll and Rubisco levels in OsNOA1-silenced plants were only slightly lower than those in WT. However, at 22°C, the silenced plants accumulated far less chlorophyll and Rubisco than WT. It was further revealed that the regulation of chlorophyll and Rubisco occurs at the anabolic level. Etiolated WT seedlings restored chlorophyll and Rubisco accumulations readily once returned to light, at either 30°C or 15°C. Etiolated OsNOA1-silenced plants accumulated chlorophyll and Rubisco to normal levels only at 30°C, and lost this ability at low temperature. On the other hand, de-etiolated OsNOA1-silenced seedlings maintained similar levels of chlorophyll and Rubisco as WT, even after being shifted to 15°C for various times. Further expression analyses identified several candidate genes, including OsPorA (NADPH: protochlorophyllide oxidoreductase A), OsrbcL (Rubisco large subunit), OsRALyase (Ribosomal RNA apurinic site specific lyase) and OsPuf4 (RNA-binding protein of the Puf family), which may be involved in OsNOA1-regulated chlorophyll biosynthesis and Rubisco formation. Overall, our results suggest OsNOA1 functions in a temperature-dependent manner to regulate chlorophyll biosynthesis, Rubisco formation and plastid development in rice.     

A reversible decrease in ribulose 1,5‐bisphosphate carboxylase/oxygenase carboxylation activity caused by the aggregation of the enzyme's large subunit is triggered in response to the exposure of moderate irradiance‐grown plants to low irradiance

Ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) is highly regulated in response to fluctuations in the environment, including changes in irradiance. However, no complex data are available on Rubisco regulatory mechanisms triggered in plants which are submitted to moderate–low irradiance shift. Therefore, we investigated in a comprehensive way the changes at the level of amount of Rubisco protein, its structural organization and carboxylase activity of the holoenzyme as triggered by exposure of moderate irradiance‐grown Arabidopsis thaliana plants to low irradiance conditions. An exposure of moderate irradiance‐grown plants to low irradiance for a single photoperiod caused the exclusion of a certain pool of Rubisco under altered conditions owing to oxidative modifications resulting in the formation of protein aggregates involving Rubisco large subunit (LS). As a result, both initial and total Rubisco carboxylase activities were reduced, whereas Rubisco activation state remained largely unchanged. The results of the determination of reactive oxygen species indicated that a moderate/low irradiance transition had stimulated ¹O₂ accumulation and we strongly suggest that Rubisco oxidative modifications leading to formation of aggregates encompassing Rubisco‐LS were triggered by ¹O₂. When moderate irradiance regime was resumed, the majority of Rubisco‐LS containing aggregates tended to be resolubilized, and this allowed Rubisco carboxylation activities to be largely recovered, without changes in the activation state of the enzyme. In the longer term, these results allow us to better understand a complexity of Rubisco regulatory mechanisms activated in response to abiotic stresses and during recovery from the stresses.     

Structure and function of Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating CO(2) into the biosphere. At the same time Rubisco is an extremely inefficient catalyst and its carboxylase activity is compromised by an opposing oxygenase activity involving atmospheric O(2). The shortcomings of Rubisco have implications for crop yield, nitrogen and water usage, and for the global carbon cycle. Numerous high-resolution crystal structures of different forms of Rubisco are now available, including structures of mutant enzymes. This review uses the information provided in these structures in a structure-based sequence alignment and discusses Rubisco function in the context of structural variations at all levels--amino acid sequence, fold, tertiary and quaternary structure--with an evolutionary perspective and an emphasis on the structural features of the enzyme that may determine its function as a carboxylase.     

水稻温敏失绿突变体的Rubisco活化酶活性、蛋白质与氨基酸组分的变化

在水稻温敏失绿突变性状表达过程中,对其Rubsico 含量、Rubsico 活化酶活性,全叶蛋白及游离氨基酸组分变化进行测定。结果表明:突变体的Rubisco 结构和含量与野生型一样,保持相对稳定;而其Rubisco 活化酶活性则随一个分子量为56.2kD(PI=4.5)的特异蛋白质的存在与消失发生明显改变。当突变性状表达时,分子量为56.2kD(PT=4.5)的特异蛋白消失,其Rubisco 活化酶活性下降;当叶片失绿区域复绿时,56.2kD(PI=4.5)特异蛋白出现,则Rubisco 活化酶活性上升。这一密切地相关关系表明,突变体的Rubisco 活化酶活性变化在光合作用过程中,除与自身结构和含量有关外,还与叶片中这一特异蛋白的存在密切相关,它可能是Rubisco 活化酶活性的调节蛋白。这种调节具体表现在氨基酸代谢上,是对上游氨基酸的阻遏调控,从而使叶绿体的结构物质合成受阻,最终导致类囊体膜的退化。     

Redox modulation of Rubisco conformation and activity through its cysteine residues

Treatment of purified Rubisco with agents that specifically oxidize cysteine-thiol groups causes catalytic inactivation and increased proteolytic sensitivity of the enzyme. It has been suggested that these redox properties may sustain a mechanism of regulating Rubisco activity and turnover during senescence or stress. Current research efforts are addressing the structural basis of the redox modulation of Rubisco and the identification of critical cysteines. Redox shifts result in Rubisco conformational changes as revealed by the alteration of its proteolytic fragmentation pattern upon oxidation. In particular, the augmented susceptibility of Rubisco to proteases is due to increased exposure of a small loop (between Ser61 and Thr68) when oxidized. Progressive oxidation of Rubisco cysteines using disulphide/thiol mixtures at different ratios have shown that inactivation occurs under milder oxidative conditions than proteolytic sensitization, suggesting the involvement of different critical cysteines. Site-directed mutagenesis of conserved cysteines in the Chlamydomonas reinhardtii Rubisco identified Cys449 and Cys459 among those involved in oxidative inactivation, and Cys172 and Cys192 as the specific target for arsenite. The physiological importance of Rubisco redox regulation is supported by the in vivo response of the cysteine mutants to stress conditions. Substitution of Cys172 caused a pronounced delay in stress-induced Rubisco degradation, while the replacement of the functionally redundant Cys449-Cys459 pair resulted in an enhanced catabolism with a faster high-molecular weight polymerization and translocation to membranes. These results suggest that several cysteines contribute to a sequence of conformational changes that trigger the different stages of Rubisco catabolism under increasing oxidative conditions.     

水稻温敏失绿突变体的Rubisco活化酶活性、蛋白质与氨基酸组分的变化

在水稻温敏失绿突变性状表达过程中,对其Rutbsico含量、Rubsico活化酶活性,全叶蛋白及游离氨基酸组分变化进行测定。结果表明：突变体的Rubisco结构和含量与野生型一样,保持相对稳定;而其Rubisco活化酶活性则随一个分子量为56．2kD(PI=4．5)的特异蛋白质的存在与消失发生明显改变。当突变性状表达时,分子量为56.2kD(PI=4．5)的特异蛋白消失,其Rubisco活化酶活性下降;当叶片失绿区域复绿时,56.2kD(PI=4．5)特异蛋白出现,则Rubisco活化酶活性上升。这一密切地相关关系表明,突变体的Rubisco活化酶活性变化在光合作用过程中,除与自身结构和含量有关外,还与叶片中这一特异蛋白的存在密切相关,它可能是Rubisco活化酶活性的调节蛋白。这种调节具体表现在氨基酸代谢上,是对上游氨基酸的阻遏调控,从而使叶绿体的结构物质合成受阻,最终导致类囊体膜的退化。     

Small Oligomers of Ribulose-bisphosphate Carboxylase/Oxygenase (Rubisco) Activase Are Required for Biological Activity

Ribulose-bisphosphate carboxylase/oxygenase (Rubisco) activase uses the energy from ATP hydrolysis to remove tight binding inhibitors from Rubisco, thus playing a key role in regulating photosynthesis in plants. Although several structures have recently added much needed structural information for different Rubisco activase enzymes, the arrangement of these subunits in solution remains unclear. In this study, we use a variety of techniques to show that Rubisco activase forms a wide range of structures in solution, ranging from monomers to much higher order species, and that the distribution of these species is highly dependent on protein concentration. The data support a model in which Rubisco activase forms an open spiraling structure rather than a closed hexameric structure. At protein concentrations of 1 μm, corresponding to the maximal activity of the enzyme, Rubisco activase has an oligomeric state of 2–4 subunits. We propose a model in which Rubisco activase requires at least 1 neighboring subunit for hydrolysis of ATP.     

Transgenic tobacco plants with improved cyanobacterial Rubisco expression but no extra assembly factors grow at near wild‐type rates if provided with elevated CO2

Introducing a carbon‐concentrating mechanism and a faster Rubisco enzyme from cyanobacteria into higher plant chloroplasts may improve photosynthetic performance by increasing the rate of CO₂ fixation while decreasing losses caused by photorespiration. We previously demonstrated that tobacco plants grow photoautotrophically using Rubisco from Synechococcus elongatus, although the plants exhibited considerably slower growth than wild‐type and required supplementary CO₂. Because of concerns that vascular plant assembly factors may not be adequate for assembly of a cyanobacterial Rubisco, prior transgenic plants included the cyanobacterial chaperone RbcX or the carboxysomal protein CcmM35. Here we show that neither RbcX nor CcmM35 is needed for assembly of active cyanobacterial Rubisco. Furthermore, by altering the gene regulatory sequences on the Rubisco transgenes, cyanobacterial Rubisco expression was enhanced and the transgenic plants grew at near wild‐type growth rates, although still requiring elevated CO₂. We performed detailed kinetic characterization of the enzymes produced with and without the RbcX and CcmM35 cyanobacterial proteins. These transgenic plants exhibit photosynthetic characteristics that confirm the predicted benefits of introduction of non‐native forms of Rubisco with higher carboxylation rate constants in vascular plants and the potential nitrogen‐use efficiency that may be achieved provided that adequate CO₂ is available near the enzyme.     

Maintaining photosynthetic CO2 fixation via protein remodelling: the Rubisco activases

The key photosynthetic, CO₂-fixing enzyme Rubisco forms inactivated complexes with its substrate ribulose 1,5-bisphosphate (RuBP) and other sugar phosphate inhibitors. The independently evolved AAA+ proteins Rubisco activase and CbbX harness energy from ATP hydrolysis to remodel Rubisco complexes, facilitating release of these inhibitors. Here, we discuss recent structural and mechanistic advances towards the understanding of protein-mediated Rubisco activation. Both activating proteins appear to form ring-shaped hexameric arrangements typical for AAA+ ATPases in their functional form, but display very different regulatory and biochemical properties. Considering the thermolability of the plant enzyme, an improved understanding of the mechanism for Rubisco activation may help in developing heat-resistant plants adapted to the challenge of global warming.     

Light-dependent development of single cell C4 photosynthesis in cotyledons of Borszczowia aralocaspica (Chenopodiaceae) during transformation from a storage to a photosynthetic organ

BACKGROUND AND AIMS: Previous work has shown that Borszczowia aralocaspica (Chenopodiaceae) accomplishes C4 photosynthesis in a unique, polarized single-cell system in leaves. Mature cotyledons have the same structure as leaves, with chlorenchyma cells having biochemical polarization of dimorphic chloroplasts and C4 functions at opposite ends of the cell. KEY RESULTS: Development of the single-celled C4 syndrome in cotyledons was characterized. In mature seeds, all cell layers are already present in the cotyledons, which contain mostly lipids and little starch. The incipient chlorenchyma cells have a few plastids towards the centre of the cell. Eight days after germination and growth in the dark, small plastids are evenly distributed around the periphery of the expanding cells. Immunolocalization studies show slight labelling of Rubisco in plastids in seeds, including chlorenchyma, hypodermal and water storage, but not epidermal, cells. After imbibition and 8 d of growth in the dark labelling for Rubisco progressively increased, being most prominent in chlorenchyma cells. There was no immunolabelling for the plastid C4 enzyme pyruvate, Pi dikinase under these conditions. Cotyledons developing in light show formation of chlorenchyma tissue, induction of the cytosolic enzyme phosphoenolpyruvate carboxylase and development of dimorphic chloroplasts at opposite ends of the cells. Proximal chloroplasts have well-developed grana, store starch and contain Rubisco; those located distally have reduced grana, lack starch and contain pyruvate, Pi dikinase. CONCLUSIONS: The results show cotyledons developing in the dark have a single structural plastid type which expresses Rubisco, while light induces formation of dimorphic chloroplasts from the single plastid pool, synthesis of C4 enzymes, and biochemical and structural polarization leading to the single-cell C4 syndrome.     

Modification of Rubisco and Altered Proteolytic Activity in O3-Stressed Hybrid Poplar (Populus maximowizii x trichocarpa)

Exposing hybrid poplar (Populus maximowizii x trichocarpa) plants to ozone (O3) resulted in an acceleration of the visual symptoms of senescence and a decrease in the activity and quantity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Whole plants, crude leaf extracts, and isolated intact chloroplasts of hybrid poplar clone 245 were used to test the hypothesis that O3-induced structural modifications of Rubisco affect the activity of this key photosynthetic enzyme. Proteolytic activity, per se, could not account for losses in Rubisco; acidic and alkaline protease activities declined or were unaffected in foliage of O3-treated poplar saplings. In vitro treatment of leaf extracts with O3 decreased total Rubisco activity and binding of the enzyme's transition-state analog, 2-carboxyarabinitol bisphosphate. Additionally, O3 increased the loss of Rubisco large subunit (LSU) when extracts were incubated at 37[deg]C. Treatment of isolated intact chloroplasts with O3 accelerated both the loss of the 55-kD Rubisco LSU and the accumulation of Rubisco LSU aggregates, as visualized by immunoblotting. The time-dependent modification in Rubisco structure was the primary response of the isolated organelles to O3 treatment, with little proteolytic degradation of the LSU detected.     

Nuclear Mutation Inhibits Expression of the Chloroplast Gene That Encodes the Large Subunit of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase

Chlamydomonas reinhardtii mutant 76-5EN was recovered as a light-sensitive, acetate-requiring strain that failed to complement a chloroplast structural gene mutant of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39). Further genetic analysis revealed that the new mutation was inherited in a mendelian pattern, indicating that it resides within the nucleus. The 76-5EN mutant lacks Rubisco holoenzyme but has wild-type levels of whole-chain electron transport activity and chlorophyll. During a 1-min pulse labeling with 35SO42-, little or no Rubisco large-subunit synthesis occurred in the mutant. Nuclear-encoded small subunits were synthesized to a normal level and were subsequently degraded. When analyzed by northern hybridization, the 76-5EN mutant was found to have a decreased level of large-subunit mRNA. Large-subunit mRNA synthesis also appeared to be reduced during a 10-min pulse labeling with [32P]orthophosphate, but the labeled mRNA was stable during a 1-h chase. These results indicate that a nuclear gene mutation specifically disrupts the accumulation of large-subunit mRNA within the chloroplast. A deeper understanding of the nature of the 76-5EN gene may be useful for manipulating the expression of the agronomically important Rubisco enzyme.     

Subunit interface dynamics in hexadecameric rubisco

Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) plays an important role in the global carbon cycle as a hub for biomass. Rubisco catalyzes not only the carboxylation of RuBP with carbon dioxide but also a competing oxygenation reaction of RuBP with a negative impact on photosynthetic yield. The functional active site is built from two large (L) subunits that form a dimer. The octameric core of four L₂ dimers is held at each end by a cluster of four small (S) subunits, forming a hexadecamer. Each large subunit contacts more than one S subunit. These interactions exploit the dynamic flexibility of Rubisco, which we address in this study. Here, we describe seven different types of interfaces of hexadecameric Rubisco. We have analyzed these interfaces with respect to the size of the interface area and the number of polar interactions, including salt bridges and hydrogen bonds in a variety of Rubisco enzymes from different organisms and different kingdoms of life, including the Rubisco-like proteins. We have also performed molecular dynamics simulations of Rubisco from Chlamydomonas reinhardtii and mutants thereof. From our computational analyses, we propose structural checkpoints of the S subunit to ensure the functionality and/or assembly of the Rubisco holoenzyme. These checkpoints appear to fine-tune the dynamics of the enzyme in a way that could influence enzyme performance.     

Insights into eukaryotic Rubisco assembly — Crystal structures of RbcX chaperones from Arabidopsis thaliana

Background

Chloroplasts were formed by uptake of cyanobacteria into eukaryotic cells ca. 1.6 billion years ago. During evolution most of the cyanobacterial genes were transferred from the chloroplast to the nuclear genome. The rbcX gene, encoding an assembly chaperone required for Rubisco biosynthesis in cyanobacteria, was duplicated. Here we demonstrate that homologous eukaryotic chaperones (AtRbcX1 and AtRbcX2) demonstrate different affinities for the C-terminus of Rubisco large subunit and determine their crystal structures.

Methods

Three-dimensional structures of AtRbcX1 and AtRbcX2 were resolved by the molecular replacement method. Equilibrium binding constants of the C-terminal RbcL peptide by AtRbcX proteins were determined by spectrofluorimetric titration. The binding mode of RbcX–RbcL was predicted using molecular dynamic simulation.

Results

We provide crystal structures of both chaperones from Arabidopsis thaliana providing the first structural insight into Rubisco assembly chaperones form higher plants. Despite the low sequence homology of eukaryotic and cyanobacterial Rubisco chaperones the eukaryotic counterparts exhibit surprisingly high similarity of the overall fold to previously determined prokaryotic structures. Modeling studies demonstrate that the overall mode of the binding of RbcL peptide is conserved among these proteins. As such, the evolution of RbcX chaperones is another example of maintaining conserved structural features despite significant drift in the primary amino acid sequence.

General significance

The presented results are the approach to elucidate the role of RbcX proteins in Rubisco assembly in higher plants.     

A conserved mechanism controls translation of Rubisco large subunit in different photosynthetic organisms

We previously proposed a mechanism for control of Rubisco expression and assembly during oxidative stress in Chlamydomonas reinhardtii. The N terminus of the large subunit (LSU) comprises an RNA recognition motif (RRM) that is normally buried in the protein, but becomes exposed under oxidizing conditions when the glutathione pool shifts toward its oxidized form. Thus, de novo translation and assembly of Rubisco LSU stop with similar kinetics and the unpaired small subunit (SSU) is rapidly degraded. Here we show that the structure of the N-terminal domain is highly conserved throughout evolution, despite its relatively low sequence similarity. Furthermore, Rubisco from a broad evolutionary range of photosynthetic organisms binds RNA under oxidizing conditions, with dissociation constant values in the nanomolar range. In line with these observations, oxidative stress indeed causes a translational arrest in land plants as well as in Rhodospirillum rubrum, a purple bacterium that lacks the SSU. We highlight an evolutionary conserved element located within alpha-helix B, which is located in the center of the RRM and is also involved in the intramolecular interactions between two LSU chains. Thus, assembly masks the N terminus of the LSU hiding the RRM. When assembly is interrupted due to structural changes that occur under oxidizing conditions or in the absence of a dedicated chaperone, the N-terminal domain can become exposed, leading to the translational arrest of Rubisco LSU. Taken together, these results support a model by which LSU translation is governed by its dimerization. In the case that regulation of type I and type II Rubisco is conserved, the SSU does not appear to be directly involved in LSU translation.