Molecular evolution of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)

Abstract The evolutionary relationship of the RuBisCO large subunit gene(s) ( rbcL ) of several prokaryotes was examined using the technique of heterologous DNA hybridization. Restriction fragments of cloned rbcL from Anacystis nidulans 6301, Chlamydomonas reinhardtii, Rhodospirillum rubrum , and maize were nick-translated and used as probes. The C. reinhardtii and maize probes hybridized with restriction fragment(s) only from cyanobacteria: Agmenellum quadruplicatum, Fremyella diplosiphon , and Mastigocladus laminosus . In addition, the A. nidulans probe hybridized with restriction fragment(s) from Alcaligenes eutrophus, Chromatium vinosum, Nitrobacter hamburgensis, Paracoccus denitrificans, Pseudomonas oxalaticus, Rhodomicrobium vannielii, Rhodopseudomonas capsulata, Rhodopseudomonas palustris, Rhodopseudomonas sphaeroides, Thiobacillus intermedius, Thiobacillus neapolitanus , and Thiothrix nivea . The elucidated fragment of Rhodopseudomonas species is presumably for the Form I RuBisCO LSU of these organisms. The R. rubrum probe hybridized only to a restriction fragment(s) from R. capsulata, R. palustris, R. sphaeroides, T. neapolitanus , and T. nivea . The fragment(s) of Rhodopseudomonas species is the Form II rbcL of these organisms. The restriction fragments of T. neapolitanus and T. nivea were also different from those elucidated by the A. nidulans probe, suggesting the presence of a second (different) rbcL in these organisms. Positive hybridization was not obtained using any of the probes with DNA from Beggiatoa alba, Chlorobium vibrioforme or Chloroflexus aurantiacus . It appears that all rbcL have evolved from a common ancestor. Our data are consistent with and supportive of the evolutionary scheme for RuBisCO proposed by Akazawa, Takabe, and Kobayashi [1].     

高温伤害光合机构原初位点的研究进展

本文介绍了高温伤害光合机构原初位点的研究进展,分析了不同观点产生的可能原因,为进一步研究高温对植物光合作用的影响提供思路。     

Characterization of rbcL group IA introns from two colonial volvocalean species (Chlorophyceae)

Group I introns were reported for the first time in the large subunit of Rubisco (rbcL) genes, using two colonial green algae, Pleodorina californica and Gonium multicoccum (Volvocales). The rbcL gene of P. californica contained an intron (PlC intron) of 1320 bp harboring an open reading frame (ORF). The G. multicoccum rbcL gene had two ORF-lacking introns of 549 (GM1 intron) and 295 (GM2 intron) base pairs. Based on the conserved nucleotide sequences of the secondary structure, the PlC and GM1 introns were assigned to group IA2 whereas the GM2 intron belonged to group IA1. Southern hybridization analyses of nuclear and chloroplast DNAs indicated that such intron-containing rbcL genes are located in the chloroplast genome. Sequencing RNAs from the two algae revealed that these introns are spliced out during mRNA maturation. In addition, the PlC and GM1 introns were inserted in the same position of the rbcL exons, and phylogenetic analysis of group IA introns indicated a close phylogenetic relationship between the PlC and GM1 introns within the lineage of bacteriophage group IA2 introns. However, P. californica and G. multicoccum occupy distinct clades in the phylogenetic trees of the colonial Volvocales, and the majority of other colonial volvocalean species do not have such introns in the rbcL genes. Therefore, these introns might have been recently inserted in the rbcL genes independently by horizontal transmission by viruses or bacteriophage.     

Rubisco genes indicate a close phylogenetic relation between the plastids of Chromophyta and Rhodophyta

The genes for both subunits of Rubisco (rbcL, rbcS) are located on the plastome of the brown alga Ectocarpus siliculosus (Chromophyta, Phaeophyceae). The organization of these genes in the form of an operon was similar to that found in rhodoplasts, cyanobacteria and the plastids of Cryptomonas . Sequence analysis of the complete operon revealed a high degree of homology and great structural similarities to corresponding genes from two red algae. In contrast, sequence homology to Rubisco genes from chloroplasts and cyanobacteria was much lower. This clearly indicated a close phylogenetic relationship between the plastids of Rhodophyta and Chromophyta which seem to have evolved independently from the chloroplasts (polyphyletic origin). Our data suggest that the plastids of Chromophyta and Cryptophyta have originated from endosymbiotic unicellular red algae. Surprisingly, red and brown algal Rubiscos show a significantly higher degree of homology to that from a hydrogen bacterium than to those from cyanobacteria.     

Regulation of Rubisco by inhibitors in the light

2-carboxy-D-arabinitol-1-phosphate (CA1P) bound to Rubisco either in leaf extracts or after purification can be displaced by SO₄^2? ions. Thus, treatment of leaf extracts with a buffer containing 200 mol m^?3 SO₄^2? displaces any bound CA1P and enables measurement of maximum car-boxylation potential. In tobacco leaves, the activity following treatment with SO₄^?2 ions (‘maximal activity’) is greater than the total Rubisco activity. The ratio of the two activities altered in a dynamic way with fluctuations in irradiance. Even in species which do not produce significant amounts of CA1P, the maximal activity greatly exceeded the total activity. Anion exchange separation of components in acid extracts confirmed the absence of CA1P in tobacco leaves harvested above an irradiance of 300 μmol quanta m^?2 s^?1, but the presence of another inhibitor of Rubisco. These results are consistent with the regulation of Rubisco activity by inhibitors other than CA1P which, like CA1P, can be displaced by SO₄^2? ions.     

Elevated CO<Subscript>2</Subscript> and temperature differentially affect photosynthesis and resource allocation in flag and penultimate leaves of wheat

Differences in acclimation to elevated growth CO₂ (700 μmol mol⁻¹, EC) and elevated temperature (ambient +4 °C, ET) in successive leaves of wheat were investigated in field chambers. At a common measurement CO₂, EC increased photosynthesis and the quantum yield of electron transport (Φ) early on in the growth of penultimate leaves, and later decreased them. In contrast, EC did not change photosynthesis, and increased Φ at later growth stages in the flag leaf. Contents of chlorophyll (Chl), ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO), and total soluble protein were initially higher and subsequently lower in penultimate than flag leaves. EC decreased RuBPCO protein content relative to soluble protein and Chl contents throughout the development of penultimate leaves. On the other hand, EC initially increased the RuBPCO:Chl and Chl a/b ratios, but later decreased them in flag leaves. In the flag leaves but not in the penultimate leaves, ET initially decreased initial and specific RuBPCO activities at ambient CO₂ (AC) and increased them at EC. Late in leaf growth, ET decreased Chl contents under AC in both kinds of leaves, and had no effect or a positive one under EC. Thus the differences between the two kinds of leaves were due to resource availability, and to EC-increased allocation of resources to photon harvesting in the penultimate leaves, but to increased allocation to carboxylation early on in growth, and to light harvesting subsequently, in the flag leaves.     

Disparate distributions of chemolithotrophs containing form IA or IC large subunit genes for ribulose-1,5-bisphosphate carboxylase/oxygenase in intertidal marine and littoral lake sediments

The distributions of bacterial form IA and form IC ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) were investigated using Lowes Cove intertidal mudflat and Damariscotta Lake littoral sediments by PCR amplification of 492-495 bp fragments of the large subunit RuBisCO gene, cbbL. Genomic extracts for amplification were obtained from lake surface (upper 2 mm), mudflat surface (upper 2 mm), subsurface (5-7 cm), and soft-shell clam (Mya arenaria) burrow-wall sediments, as well as from a sulfide-oxidizing mat. Phylogenetic analyses of cbbL clone libraries revealed that Lowes Cove sediments were dominated by form IA cbbL-containing sequences most closely related to cbbL genes of sulfur-oxidizing bacteria or sulfide-oxidizing mats. In contrast, Damariscotta Lake cbbL clones contained primarily form IC cbbL sequences, which typify aerobic CO- and hydrogen-oxidizing facultative chemolithotrophs. Statistical analyses supported clear differentiation of intertidal and lake chemolithotroph communities, and provided evidence for some differentiation among intertidal communities. amova and libshuff analyses of Lowes Cove libraries suggested that M. arenaria burrow-wall sediments did not harbour distinct communities compared with surface and subsurface sediments, but that surface and subsurface libraries displayed moderate differences. The results collectively support a conceptual model in which the relative distribution of form IA- and IC-containing bacterial chemolithotrophs depends on sulfide availability, which could reflect the role of sulfate reduction in sediment organic matter metabolism, or the presence of geothermal sulfide sources.     

Small-angle X-ray study on the structure of ribulose-1,5-bisphosphate carboxylase-oxygenase from Rhodospirillum rubrum

The quaternary structure of ribulose-1,5-bisphosphate carboxylase-oxygenase (rubisco) from Rhodospirillum rubrum, an enzyme consisting of two large subunits, L₂, was investigated by small-angle X-ray scattering. In the presence of HCO ₃ ^- and Mg²⁺, rubisco is in the active state and displays a radius of gyration of 2.96 nm, a maximum diameter of 9.5 nm and a volume of 170 nm³. A model is presented where the subunits are arranged back-to-back, rotated relative to each other by 90°, and shifted by 1.3 nm. Upon inactivation by removal of HCO ₃ ^- and Mg²⁺, the model swells slightly without any distinct changes in configuration. This contrasts with our previous observations with rubisco from Alcaligenes eutrophus, an enzyme composed of small (S) and large (L) subunits, L₈S₈, where inactivation gives rise to substantial changes in configuration.Abbreviations RuBP Ribulose-1,5-bisphosphate - 3-PGA 3-phosphoglyceric acid     

UV-B response of green and etiolated barley seedlings

7-d-old etiolated and green barley seedlings (Hordeum vulgare L. cv. Alfa) were irradiated with UV-B for 30 min and then kept for 24 h in light or darkness. Chlorophyll (Chl) synthesis was inhibited by about 30 % as a result of UV-B irradiation, but there were no significant changes in photochemical activity measured by variable to maximum fluorescence ratio (F_v/F_m), quantum yield (Φ_PS2) and oxygen evolution rate. Electron transport of etiolated seedlings was similar to that of green ones, nevertheless, the Chl content was more then 2-fold lower. Ribulose-1,5-bisphosphate carboxylase/oxygenase large and small subunits were diminished as a result of UV-B irradiation in etiolated and green plants, especially in those kept in the darkness. Catalase activity decreased and total superoxide dismutase activity increased in green and etiolated plants following UV-B treatment. When benzidine was used as a substrate, an isoform located between guaiacol peroxidases 2 and 3 (guaiacol peroxidase X) appeared, which was specific for UV-B treatment. As a result of irradiation, the contents of UV-B absorbing and UV-B induced compounds increased in green seedlings but not in etiolated seedlings.     

Experimental and theoretical study on high temperature induced changes in chlorophyll <Emphasis Type="Italic">a</Emphasis> fluorescence oscillations in barley leaves upon 2 % CO<Subscript>2</Subscript>

Oscillations in many of photosynthetic quantities with a period of about 1 min can be routinely measured with higher plant leaves after perturbation of the steady state by sudden change in gas phase. Among all hypotheses suggested so far to explain the oscillations, an effect of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) activation status to control the oscillations is highly probable, at least upon high temperature (HT) treatment when in vivo RuBPCO activity controlled by RuBPCO activase (RuBPCO-A) decreases. Therefore, we measured the oscillations in fluorescence signal coming from barley leaves (Hordeum vulgare L. cv. Akcent) after their exposure for various time intervals to different HTs in darkness. We also evaluated steady state fluorescence and CO₂ exchange parameters to have an insight to functions of electron transport chain within thylakoid membrane and Calvin cycle before initiation of the oscillations. The changes in period of the oscillations induced by moderate HT (up to 43 °C) best correlated with changes in non-photochemical fluorescence quenching (q_N) that in turn correlated with changes in gross photosynthetic rate (P _G) and rate of RuBPCO activation (k_act). Therefore, we suggest that changes in period of the oscillations caused by moderate HT are mainly controlled by RuBPCO activation status. For more severe HT (45 °C), the oscillations disappeared which was probably caused by an insufficient formation of NADPH by electron transport chain within thylakoid membrane as judged from a decrease in photochemical fluorescence quenching (q_P). Suggestions made on the basis of experimental data were verified by theoretical simulations of the oscillations based on a model of Calvin cycle and by means of a control analysis of the model.     

PHYLOGENY OF THE BATRACHOSPERMALES (RHODOPHYTA) INFERRED FROM rbcL AND 18S RIBOSOMAL DNA GENE SEQUENCES

The sequence data from the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase ( rbc L) gene and 18S ribosomal DNA (small subunit) of taxa in the freshwater rhodophyte order Batrachospermales were used to construct phylogenetic hypotheses. Taxa examined in this study represent four families, eight genera, and six sections of the genus Batrachospermum . In addition, Rhododraparnaldia oregonica Sheath, Whittick et Cole, was included in the analysis because it shares particular ultrastructural, reproductive, and morphological characteristics with members of the Batrachospermales and Acrochaetiales. The trees generated from each gene, as well as a combined data set, were largely congruent. Rhododraparnaldia consistently occurs on an early branch within the Acrochaetiales – Palmariales clade and does not appear to be a member of the Batrachospermales. In addition, Thorea violacea Bory de St. Vincent was not closely related to the other taxa of the Batrachospermales in all trees and hence the family Thoreaceae does not appear to be a natural grouping within this order. All other taxa analyzed, which are presently classified within this order, formed a monophyletic clade in most analyses. Psilosiphon scoparium Entwisle was not closely allied with the taxa of the Lemaneaceae, lending support to the newly proposed family Psilosiphonaceae. Sequence data from the remaining taxa of the Lemaneaceae support the concept of a derived monophyletic clade. The genus Batrachospermum appears to comprise many morphologically similar but distantly related taxa, which will need further investigation to resolve their taxonomic status. Tuomeya, Sirodotia and Nothocladus are retained at the generic level until further data are obtained.     

Potential Consequences of Virus Infection for Shade-Sun Acclimation in Leaves

Attention is drawn to literature evidence that leaf virus infection may interfere with synthesis of ribulose-1,5-bisphosphate carboxylase oxygenase, and with the activity of photosystem II, two main requirements for shade-sun acclimation. Preliminary experiments which show that virus infections resulting in these interactions can lead to photosynthetic physiology diagnostic of nitrogen limited plants and/or shade ecotypes are presented. Other observations on the diversity of virus infections in sun populations of wild species commonly found in the shade are presented. Together, this evidence leads to the hypothesis that virus infection may well confine individuals of some species to shaded habitats because infection prevents acclimation to bright light, and predisposes them to photoinhibition.     

The photosynthetic irradiance-response of Norway spruce exposed to a long-term elevation of CO2 concentration

During an open-top chamber experiment performed in a mountain stand of young (12-year-old) Norway spruce (Picea abies [L.] Karst.), the trees were exposed to one of two CO² concentrations (ambient CO², AC, or AC + 350 μmol mol-1 = elevated CO₂, EC) continuously over three growing seasons. To evaluate the EC influence, measurements of the relations between the rate of net CO₂ uptake (P _N ) and incidental photosynthetically active photon flux density (PPFD), as well as the content of photosynthetic pigments and chlorophyll (Chl) a fluorescence were taken in the third growing season. The short-term response to EC was evident mainly on ribulose-1,5-bisphosphate carboxylase/oxygenase kinetics without any significant change to the utilization of radiant energy. The long-term effect of EC was responsible for a decrease in P _N , content of Chl a + b, Fv/Fm ratio, quantum yield of fluorescence, and photochemical quenching. Changes of stoichiometry between the electron transport, Calvin cycle and the end-product synthesis were confirmed for responses to the long-term import of EC and led to a definition of the photosynthetic acclimation to EC in Norway spruce. This revised version was published online in August 2006 with corrections to the Cover Date.     

Effects of biomin and algae suspensions on the activities of carboxylating and decarboxylating enzymes in cadmium-treated pea plants

Cadmium-treated pea plants exhibited PEPC and NADP-ME activities, titratable acidity, and malate concentration in the leaves similar to controls. The PEPC activity in the roots of Cd-treated plants decreased by about 40 %, and NADP-ME increased more than twice. The titratable acidity remained similar as in the leaves, but the malate content diminished by about 30 %. The application of 500 g(d.m.) m-3 biomin and a combination of biomin and algae suspensions to Cd-treated plants brought about an increase in the titratable acidity and in the malate concentrations in the leaves and the roots. This revised version was published online in August 2006 with corrections to the Cover Date.     

The carboxylase activity of Rubisco and the photosynthetic performance in aquatic plants

Summary Activated carboxylase activities of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), as well as photosynthetic rates were measured for 42 species of freshwater and marine macrophytes. While the carboxylase activity varied greatly among the species investigated (0.2–12.5 mol CO₂ mg^–1 chlorophyll min^–1), the submersed freshwater plants showed significantly lower activities than emergent, floating leaved or secondary submersed forms. The variability in photosynthetic rates correlated with the carboxylase activity only for the marine macroalgae, and their photosynthesis to carboxylase activity ratios were close to 1. These plants also had a consistently high inorganic carbon transport capability, and it is suggested that ribulose-1,5-bisphosphate carboxylase/oxygenase activity is an important internal factor regulating the photosynthetic capacity within this plant group where, apparently, the internal CO₂ concentration is high and photorespiration is suppressed. Among the freshwater forms, it appears that their much lower inorganic carbon transport ability, rather than their carboxylase activity, limits the photosynthetic process.     

The mechanism of Rubisco activase: Insights from studies of the properties and structure of the enzyme

Rubisco, the primary carboxylating enzyme in photosynthesis, must be activated to catalyze CO₂ fixation. The concept of an activase, a specific protein for activating Rubisco, was first introduced in 1985 based largely on biochemical and genetic studies of a high CO₂-requiring mutant of Arabidopsis (Salvucci et al. (1985) Photosynth Res 7: 193–201). Over the past ten years, details about the occurrence, structure, and properties of Rubisco activase have been elucidated. However, the mechanism of action of Rubisco activase remains elusive. This review discusses the need for and function of Rubisco activase and summarizes information about the properties and structure of Rubisco activase. The information is evaluated in the context of the mechanism of Rubisco activase.Abbreviations CA1-P carboxyarabinitol 1-phosphate - PS photosystem - Rubisco ribulose 1,5-bisphosphate carboxylase/oxygenase - RuBP ribulose 1,5-bisphosphate - XuBP xylulose 1,5-bisphosphate The US Government right to retain a non-exclusive, royalty-free licence in and to any copyright is acknowledged.     

Identification and Structural Analysis of a Novel Carboxysome Shell Protein with Implications for Metabolite Transport

Bacterial microcompartments (BMCs) are polyhedral bodies, composed entirely of proteins, that function as organelles in bacteria; they promote subcellular processes by encapsulating and co-localizing targeted enzymes with their substrates. The best-characterized BMC is the carboxysome, a central part of the carbon-concentrating mechanism that greatly enhances carbon fixation in cyanobacteria and some chemoautotrophs. Here we report the first structural insights into the carboxysome of Prochlorococcus, the numerically dominant cyanobacterium in the world's oligotrophic oceans. Bioinformatic methods, substantiated by analysis of gene expression data, were used to identify a new carboxysome shell component, CsoS1D, in the genome of Prochlorococcus strain MED4; orthologs were subsequently found in all cyanobacteria. Two independent crystal structures of Prochlorococcus MED4 CsoS1D reveal three features not seen in any BMC-domain protein structure solved to date. First, CsoS1D is composed of a fused pair of BMC domains. Second, this double-domain protein trimerizes to form a novel pseudohexameric building block for incorporation into the carboxysome shell, and the trimers further dimerize, forming a two-tiered shell building block. Third, and most strikingly, the large pore formed at the 3-fold axis of symmetry appears to be gated. Each dimer of trimers contains one trimer with an open pore and one whose pore is obstructed due to side-chain conformations of two residues that are invariant among all CsoS1D orthologs. This is the first evidence of the potential for gated transport across the carboxysome shell and reveals a new type of building block for BMC shells.     

Phylogeny of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Genes in Haloalkaliphilic Obligately Autotrophic Sulfur-Oxidizing Bacteria of the Genus <Emphasis Type="Italic">Thioalkalivibrio</Emphasis>

Fragments of genes of the “green-like” form I ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) of eight species of haloalkaliphilic obligately autotrophic sulfur-oxidizing bacteria of the genus Thioalkalivibrio have been revealed and sequenced using previously developed oligonucleotide primers. The data obtained are used for the construction of phylogenetic trees on the basis of nucleotide sequences of RuBisCO genes and their conceptual translations into amino acid sequences. Comparative analysis of the 16S rRNA and RuBisCO gene trees reveals discrepancies between their topologies. According to a RuBisCO gene analysis, the genus Thioalkalivibrio is not monophyletic, and its inner divergence conforms to the significant morphological differences observed between the species. Presumably, horizontal (interspecies) gene transfer was involved in the evolution of the genus Thioalkalivibrio.__________Translated from Mikrobiologiya, Vol. 74, No. 3, 2005, pp. 378–386.Original Russian Text Copyright © 2005 by Tourova, Spiridonova, Berg, Kuznetsov, Sorokin.     

Photosynthetic Enzymes of the C4 Grass Setaria sphacelata Under Water Stress: A Comparison Between Rapidly and Slowly Imposed Water Deficit

Two stress imposing systems were used: a rapid stress developed by allowing excised leaves to loose water by transpiration, and a slow stress developed by withholding watering of potted plants. Carboxylating enzymes reacted differently on both types of stress. Rapid stress increased ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) activation, but both activities (initial and total) showed little variation with stress. Under slow stress the activation did not change, although both activities decreased much under stress. Phosphoenolpyruvate carboxylase (PEPC) showed a deep decrease of activity under rapid stress, nevertheless, a certain recovery was found under extreme stress. On the other hand, under slow stress the activity of PEPC showed a linear increase with decreasing relative water content. The ratio between physiological and maximal activity increased slightly under both types of stress. The activity of malic enzyme did not change under rapid stress, and decreased linearly under slow stress.