Kegg Pathway: Carbon fixation

Angew Chem Int Ed Engl. 2008 Jul 22;
Yin SF, Maruyama J, Yamashita T, Shimada S

Physiol Plant. 2008 Jul 8;
Maayan I, Shaya F, Ratner K, Mani Y, Lavee S, Avidan B, Shahak Y, Ostersetzer-Biran O

Olive leaves are known to mature slowly, reaching their maximum photosynthetic activity only after full leaf expansion. Poor assimilation rates, typical to young olive leaves, were previously associated with low stomata conductance. Yet, very little is known about chloroplast biogenesis throughout olive leaf development. Here, the photosynthetic activity and plastids development throughout leaf maturation is characterized by biochemical and ultrastructural analyses. Although demonstrated only low photosynthetic activity, the plastids found in young leaves accumulated both photosynthetic pigments and proteins, required for photophosphorylation and Carbon fixation. However, Rubisco, which catalyzes the first major step of Carbon fixation and one of the most abundant proteins in plants, could not be detected in the young leaves and only slowly accumulated throughout development. In fact, Rubisco levels seemed tightly correlated with the observed photosynthetic activities. Yet, unlike Rubisco, numerous proteins accumulated in young olive leaves. These included the early light induced proteins (ELIPs), which may be required to reduce the risk of photodamage, due to light absorption by photosynthetic pigments. Also, high levels of ribosomal L11 subunit, transcription factor elF-5A, Histones H2B and H4 were observed in the apical leaves, and in particular a plastidic-like aldolase, which accounted for approximately 30% of the total proteins. These proteins may up regulate in their levels in order to accommodate the high demand for metabolic energy in the young developing plant tissue, further demonstrating the complex sink-to-source relationship between young and photosynthetically-active mature leaves.

Science. 2008 Jul 18; 321(5887): 342; author reply 342
Ettema TJ, Andersson SG

Berg et al. (Reports, 14 December 2007, p. 1782) reported the discovery of an autotrophic Carbon dioxide-fixation pathway in Archaea and implicated a substantial role of this pathway in global Carbon cycling based on sequence analysis of Global Ocean Sampling data. We question the validity of the latter claim.

Environ Microbiol. 2008 Jun 17;
Pierce E, Xie G, Barabote RD, Saunders E, Han CS, Detter JC, Richardson P, Brettin TS, Das A, Ljungdahl LG, Ragsdale SW

This paper describes the genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum), which is the model acetogenic bacterium that has been widely used for elucidating the Wood-Ljungdahl pathway of CO and CO(2) fixation. This pathway, which is also known as the reductive acetyl-CoA pathway, allows acetogenic (often called homoacetogenic) bacteria to convert glucose stoichiometrically into 3 mol of acetate and to grow autotrophically using H(2) and CO as electron donors and CO(2) as an electron acceptor. Methanogenic archaea use this pathway in reverse to grow by converting acetate into methane and CO(2). Acetogenic bacteria also couple the Wood-Ljungdahl pathway to a variety of other pathways to allow the metabolism of a wide variety of Carbon sources and electron donors (sugars, carboxylic acids, alcohols and aromatic compounds) and electron acceptors (CO(2), nitrate, nitrite, thiosulfate, dimethylsulfoxide and aromatic carboxyl groups). The genome consists of a single circular 2 628 784 bp chromosome encoding 2615 open reading frames (ORFs), which includes 2523 predicted protein-encoding genes. Of these, 1834 genes (70.13%) have been assigned tentative functions, 665 (25.43%) matched genes of unknown function, and the remaining 24 (0.92%) had no database match. A total of 2384 (91.17%) of the ORFs in the M. thermoacetica genome can be grouped in orthologue clusters. This first genome sequence of an acetogenic bacterium provides important information related to how acetogens engage their extreme metabolic diversity by switching among different Carbon substrates and electron donors/acceptors and how they conserve energy by anaerobic respiration. Our genome analysis indicates that the key genetic trait for homoacetogenesis is the core acs gene cluster of the Wood-Ljungdahl pathway.

FEMS Microbiol Ecol. 2008 Jul 5;
Ratcliff WC, Kadam SV, Denison RF

The Carbon that rhizobia in root nodules receive from their host powers both N(2) fixation, which mainly benefits the host, and rhizobium reproduction. Rhizobia also store energy in the lipid poly-3-hydroxybutyrate (PHB), which may enhance rhizobium survival when they are Carbon limited, either in nodules or in the soil between hosts. There can be a conflict of interest between rhizobia and legumes over the rate of PHB accumulation, due to a metabolic tradeoff between N(2) fixation and PHB accumulation. To quantify the benefits of PHB to Carbon-limited rhizobia, populations of genetically uniform rhizobia with high vs. low PHB (confirmed by flow cytometry) were generated by fractionating Sinorhizobium meliloti via density gradient centrifugation, and also by harvesting cells at early vs. late stationary phase. These rhizobia were starved for 165 days. PHB use during starvation was highly predictive of both initial reproduction and long-term population maintenance. Cultured S. meliloti accumulated enough PHB to triple their initial population size when starved, and to persist for c. 150 days before the population fell below its initial value. During the first 21 days of nodule growth, undifferentiated S. meliloti within alfalfa nodules accumulated enough PHB to support significant increases in reproduction and survival during starvation.

ChemSusChem. 2008; 1(1-2): 67-70
Wong WL, Chan PH, Zhou ZY, Lee KH, Cheung KC, Wong KY

ChemSusChem. 2008; 1(3): 205-9
Chu D, Qin G, Yuan X, Xu M, Zheng P, Lu J

The electrocatalytic synthesis of low-density polyethylene (LDPE) from Carbon dioxide on a nanostructured (ns)TiO2 film electrode was investigated by controlled potential electrolysis in a solvent mixture of water and the ionic liquid 1-ethyl-3-methylimidazolium tetrafluoroborate ([EMI]BF4) at room temperature under ambient pressure. Under these conditions, the nsTiO2 film is remarkably efficient and selective for the electroreduction of CO2. The current efficiency for the formation of the electrolytic product is about 8-14% at -1.50 V (vs SCE). The electrocatalytic activity of the electrode in the electrochemical reduction of CO2 was investigated by cyclic voltammetry (CV), and the probable electrode reaction mechanism is discussed.

J Mol Microbiol Biotechnol. 2008 Jul 1;
Beyer S, Gilch S, Meyer O, Schmidt I

Nitrosomonas europaea can grow under conditions of chemolithoautotrophic aerobic (oxygen as oxidant) as well as anaerobic [nitrogen dioxide (NO(2)) as oxidant] nitrification or chemoorganotrophic anaerobic pyruvate-dependent denitrification. In this study, the adaptation of the transcription (mRNA synthesis/concentration) of N. europaea to aerobic and anaerobic growth conditions was evaluated and the transcription of genes coding for metabolic key functions was analyzed: nitrogen and energy metabolism (amoA, hao, rh1, nirK, norB, nsc, aceE, ldhA, ppc, gltA, odhA, coxA), Carbon dioxide fixation (cbbL), gluconeogenesis (ppsA), cell growth (ftsZ), and oxidative stress (sodB). During aerobic ammonia oxidation the specific activities of ammonia oxidation, nitrite reduction, and the growth rates correlated with the transcription level of the corresponding genes amoA/hao, nirK/norB/nsc, and cbbL/ftsZ. In anaerobically ammonia-oxidizing cells of N. europaea, the cellular mRNA concentrations of amoA, hao, rh1,coxA, cbbL, ftsZ, and sodB were reduced compared with aerobically nitrifying cells, but the mRNA levels of nirK, norB, and nsc were significantly increased. During anaerobic pyruvate-dependent denitrification, the mRNA abundance of nirK, norB, nsc, aceE, gltA, and odhA was increased, while the concentrations of amoA,hao, rh1, coxAcbbL, ftsZ, and sodB were significantly reduced. Temperature, pH value, and NH(4)(+), O(2), NO, and NO(2) concentrations had comparatively small effects on the transcription of the studied genes.

Biol Bull. 2008 Jun; 214(3): 255-65
Nyholm SV, Robidart J, Girguis PR

Deep-sea hydrothermal vents host highly productive ecosystems. Many of these communities are dominated by vestimentiferan tubeworms that house endosymbiotic chemoautotrophic bacteria that provide the hosts with their primary nutritional needs. Rates of Carbon fixation by these symbioses are also among the highest recorded. Despite the breadth of physiological and biochemical research on these associations, the underlying molecular mechanisms that regulate host and symbiont metabolite flux and Carbon fixation are largely unknown. Here we present metabolite flux and transcriptomics data from shipboard high-pressure respirometry experiments in which we maintained Ridgeia piscesae tubeworms at conditions comparable to those in situ. Host trophosome was used for cDNA library construction and sequencing. Of the 19,132 clones sequenced, 10,684 represented unique expressed sequence tags (ESTs). The highest proportions of genes are involved with translation, ribosomal structure and biogenesis, cellular processing, and signal transduction. There was moderate representation of genes involved in metabolite exchange and acid-base regulation. These data represent the first concomitant surveys of metabolite flux rates and gene expression for a chemoautotrophic symbiosis during net autotrophy, and they suggest that-in the case of Ridgeia piscesae-host-symbiont interactions such as cell cycle regulation may play a significant role in maintaining physiological poise during high productivity.

J Plant Physiol. 2008 Jun 19;
Conde C, Delrot S, Gerós H

Since ancient times the olive tree (Olea europaea), an evergreen drought- and moderately salt-tolerant species, has been cultivated for its oil and fruit in the Mediterranean basin. Olive is unique among the commercial important oil crops for many reasons. Today, it ranks sixth in the world's production of vegetable oils. Due to its nutritional quality, olive oil has a high commercial value compared with most other plant oils. Olive oil has a well-balanced composition of fatty acids, with small amounts of palmitate, and it is highly enriched in the moneonic acid oleate. This makes it both fairly stable against auto-oxidation and suitable for human health. Nevertheless, it is the presence of minor components, in particular phenolics, contributing for oil's high oxidative stability, color and flavor, that makes olive oil unique among other oils. Moreover, as a result of their demonstrated roles in the prevention of cancer and cardiovascular diseases, olive phenolics have gained much attention during the past years. Also unique to virgin olive oil is its characteristic aroma. This results from the formation of volatile compounds, namely, aldehydes and alcohols of six Carbon atoms, which is triggered when olives are crushed during the process of oil extraction. The biochemistry of the olive tree is also singular. O. europaea is one of the few species able to synthesize both polyols (mannitol) and oligosaccharides (raffinose and stachyose) as the final products of the photosynthetic CO(2) fixation in the leaf. These carbohydrates, together with sucrose, can be exported from leaves to fruits to fulfill cellular metabolic requirements and act as precursors to oil synthesis. Additionally, developing olives contain active chloroplasts capable of fixing CO(2) and thus contributing to the Carbon economy of the fruit. The overall quality of table olives and olive oil is influenced by the fruit ripening stage. Olive fruit ripening is a combination of physiological and biochemical changes influenced by several environmental and cultural conditions, even if most events are under strict genetic control.

J Plant Physiol. 2008 Jun 18;
Liu X, Huang B

Photosynthetic responses to increasing temperatures play important roles in regulating heat tolerance. The objectives of this study were to determine photosynthetic acclimation to increasing temperatures for creeping bentgrass (Agrostis stolonifera L.) and to examine changes in major photosynthetic components (photosynthetic pigments, photochemical efficiency, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) activity, and activation state of rubisco) involved in heat responses of photosynthesis. 'Penncross' was exposed to 20, 25, 30, and 35 degrees C for 7d at each temperature (acclimated) before being exposed to 40 degrees C for 28d or directly exposed to 40 degrees C for 28d from 20 degrees C (non-acclimated) in growth chambers. Leaf net photosynthetic rate (Pn), photochemical efficiency, rubisco activity, rubisco activation state, chlorophyll content, and carotenoid content decreased when grasses were subjected to severe heat stress at 40 degrees C for 28d. The declines in rubisco activity and activation state were most dramatic among different photosynthetic components examined in this study. Heat-acclimated plants were able to maintain significantly higher Pn, the content of chlorophyll and carotenoid, and the level of rubisco activity and activation state during subsequent exposure to severe heat stress, compared to non-acclimated plants. These results suggested that photosynthetic acclimation to increasing temperatures contributed to creeping bentgrass tolerance to severe heat stress, which was associated with the maintenance of both higher light-harvesting capacity and Carbon fixation activity during heat stress.

J Proteome Res. 2008 Jun 21;
Selao TT, Nordlund S, Norén A

Forty-four differentially expressed proteins have been identified in the photosynthetic diazotroph Rhodospirillum rubrum grown anaerobic and photoheterotrophically, with different nitrogen sources, using 2D-PAGE and MALDI-TOF, from gels containing an average of 679 +/- 52 (in N (+)) and 619 +/- 37 (in N (-)) protein spots for each gel. A higher level of expression was found under nitrogen-rich growth, for proteins involved in Carbon metabolism (reductive tricarboxylic acid cycle, CO 2 fixation, and poly-beta-hydroxybutyrate metabolism) and amino acid metabolism. The key enzymes RuBisCO and alpha-ketoglutarate synthase were found to be present in higher amounts in nitrogen-rich conditions. Ntr and Nif regulated proteins, such as glutamine synthetase and nitrogenase, were, as expected, induced under nitrogen-fixing conditions and glutamate dehydrogenase was down regulated. A novel 2Fe-2S ferredoxin with unknown function was identified from nitrogen-fixing cultures. In addition to differential expression, two of the identified proteins revealed variable p I values in response to the nitrogen source used.

Environ Microbiol. 2008 Jun 16;
Goffredi SK, Jones WJ, Erhlich H, Springer A, Vrijenhoek RC

The Yeti crab, Kiwa hirsuta Macpherson et al., is the single known species in a recently discovered crab family Kiwaidae (Decapoda: Galatheoidea) from deep-sea hydrothermal vents. Its chelipeds, walking legs and the ventral surface of its cephalothorax are covered with dense setae that, in turn, are covered with clusters of filamentous bacteria, making the crab appear extraordinarily 'hairy'. Electron microscopy revealed dense bacterial clusters attached to the chitinous outer layer of the setae. Molecular phylogenetic analyses revealed the setae-associated bacteria to be dominated by epsilon-Proteobacteria ( approximately 56% of the recovered ribotypes), gamma-Proteobacteria ( approximately 25%) and Bacteroidetes ( approximately 10%). Fluorescence in situ microscopy confirmed the attachment of filamentous epsilon-Proteobacteria on setae, but no specialized morphological structures appeared to exist for bacterial attachment. Key enzymes involved in the reductive tricarboxylic acid cycle (ATP-dependent citrate lyase) and sulfite oxidation or dissimilatory sulfate reduction (bidirectional APS reductase) were detected. Consequently, the potential for Carbon fixation and cycling of reduced and oxidized sulfur appear to exist in the dense microflora that grows on the crab's setae.

Nature. 2008 Jul 17; 454(7202): 327-30
Houlton BZ, Wang YP, Vitousek PM, Field CB

Dinitrogen (N(2)) fixation is widely recognized as an important process in controlling ecosystem responses to global environmental change, both today and in the past; however, significant discrepancies exist between theory and observations of patterns of N(2) fixation across major sectors of the land biosphere. A question remains as to why symbiotic N(2)-fixing plants are more abundant in vast areas of the tropics than in many of the mature forests that seem to be nitrogen-limited in the temperate and boreal zones. Here we present a unifying framework for terrestrial N(2) fixation that can explain the geographic occurrence of N(2) fixers across diverse biomes and at the global scale. By examining trade-offs inherent in plant Carbon, nitrogen and phosphorus capture, we find a clear advantage to symbiotic N(2) fixers in phosphorus-limited tropical savannas and lowland tropical forests. The ability of N(2) fixers to invest nitrogen into phosphorus acquisition seems vital to sustained N(2) fixation in phosphorus-limited tropical ecosystems. In contrast, modern-day temperatures seem to constrain N(2) fixation rates and N(2)-fixing species from mature forests in the high latitudes. We propose that an analysis that couples biogeochemical cycling and biophysical mechanisms is sufficient to explain the principal geographical patterns of symbiotic N(2) fixation on land, thus providing a basis for predicting the response of nutrient-limited ecosystems to climate change and increasing atmospheric CO(2).

Environ Microbiol. 2008 Jun 12;
Auguet JC, Borrego CM, Bañeras L, Casamayor EO

We designed and tested a set of specific primers for specific PCR amplification of the biotin carboxylase subunit gene (accC) of the Acetyl CoA carboxylase (ACCase) enzyme. The primer set yielded a PCR product of c. 460 bp that was suitable for denaturing gradient gel electrophoresis (DGGE) fingerprinting followed by direct sequencing of excised DGGE bands and sequence analysis. Optimization of PCR conditions for selective amplification was carried out with pure cultures of different bacteria and archaea, and laboratory enrichments. Next, fingerprinting comparisons were done in several aerobic and anaerobic freshwater planktonic samples. The DGGE fingerprints showed between 2 and 19 bands in the different samples, and the primer set provided specific amplification in both pure cultures and natural samples. Most of the samples had sequences grouped with bacterial accC, hypothetically related to the anaplerotic fixation of inorganic Carbon. Some other samples, however, yielded accC gene sequences that clustered with Crenarchaeota and were related to the 3-hydroxypropionate/4-hydroxybutyrate cycle of autotrophic crenarchaeota. Such samples came from oligotrophic high mountain lakes and the hypolimnia of a sulfide-rich lake, where crenarchaeotal populations had been previously reported by 16S rRNA surveys. This study provided a fast tool to look for presence of accC genes in natural environments as potential marker for studies of Carbon dioxide assimilation in the dark. After further refinement for better specificity against archaea, the new and novel primers could be very helpful to establish a target for crenarchaeota with implications for our understanding of archaeal Carbon biogeochemistry.

Proc Natl Acad Sci U S A. 2008 Jun 24; 105(25): 8724-9
González JM, Fernández-Gómez B, Fernàndez-Guerra A, Gómez-Consarnau L, Sánchez O, Coll-Lladó M, Del Campo J, Escudero L, Rodríguez-Martínez R, Alonso-Sáez L, Latasa M, Paulsen I, Nedashkovskaya O, Lekunberri I, Pinhassi J, Pedrós-Alió C

Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO(2) fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic Carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in Carbon-cycling.

Appl Environ Microbiol. 2008 Jun 6;
Hall JR, Mitchell KR, Jackson-Weaver O, Kooser AS, Cron BR, Crossey LJ, Takacs-Vesbach CD

The diversity and distribution of a bacterial community from Coffee Pots Hot Spring, a thermal spring in Yellowstone National Park with a temperature range of 39.3 to 74.1 degrees C and pH range of 5.75 to 6.91, was investigated by sequencing cloned PCR products and real time PCR (qPCR) of 16S rRNA and metabolic genes. The spring was inhabited by three Aquificae genera, Thermocrinis, Hydrogenobaculum, and Sulfurihydrogenibium, and members of the alpha-, beta-, and delta-Proteobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, and Candidate Division OP5. The in situ chemical affinities were calculated for 41 potential metabolic reactions using measured environmental parameters and a range of hydrogen and oxygen concentrations. Reactions that use oxygen, ferric iron, sulfur, and nitrate as electron acceptors were predicted to be the most energetically favorable, while reactions using sulfate were expected to be less favorable. Samples were screened for genes used in ammonia oxidation (amoA, bacterial gene only), the reductive tricarboxylic acid (rTCA) cycle (aclB), the Calvin cycle (cbbM), sulfate reduction (dsrAB), nitrogen fixation (nifH), nitrite reduction (nirK), and sulfide oxidation (soxEF1) by PCR. Genes for Carbon fixation by the rTCA cycle and nitrogen fixation were detected. All aclB sequences were phylogenetically related and spatially correlated to Sulfurihydrogenibium 16S rDNA sequences using qPCR (R(2) = 0.99). This result supports the recent finding of citrate cleavage by enzymes other than ATP citrate lyase in the rTCA cycle of the Aquificaceae family. We briefly consider potential biochemical mechanisms that may allow Sulfurihydrogenibium and Thermocrinis to co-dominate some hydrothermal environments.

New Phytol. 2008 Jun 4;
Nocito FF, Espen L, Crema B, Cocucci M, Sacchi GA

* Cadmium (Cd) stress increases cell metabolic demand for sulfur, reducing equivalents, and Carbon skeletons, to sustain phytochelatin biosynthesis for Cd detoxification. In this condition the induction of potentially acidifying anaplerotic metabolism in root tissues may be expected. For these reasons the effects of Cd accumulation on anaplerotic metabolism, glycolysis, and cell pH control mechanisms were investigated in maize (Zea mays) roots. * The study compared root apical segments, excised from plants grown for 24 h in a nutrient solution supplemented, or not, with 10 microm CdCl(2), using physiological, biochemical and (31)P-nuclear magnetic resonance (NMR) approaches. * Cadmium exposure resulted in a significant decrease in both cytosolic and vacuolar pH of root cells and in a concomitant increase in the Carbon fluxes through anaplerotic metabolism leading to malate biosynthesis, as suggested by changes in dark CO(2) fixation, metabolite levels and enzyme activities along glycolysis, and mitochondrial alternative respiration capacity. This scenario was accompanied by a decrease in the net H(+) efflux from the roots, probably related to changes in plasma membrane permeability. * It is concluded that anaplerotic metabolism triggered by Cd detoxification processes might lead to an imbalance in H(+) production and consumption, and then to cell acidosis.

Ying Yong Sheng Tai Xue Bao. 2008 Mar; 19(3): 647-52
Ren LL, Ling WT, Gao YZ

This paper studied the enhanced fixation of phenanthrene in clay loam soil, sandy silt soil, and silt loam soil under effects of exotic organic materials (EOMs) commercial organic fertilizer and peat. The results showed that after the addition of EOMs, the adsorption isotherms of phenanthrene in test soils were still linear, and distribution was the predominant mechanism for phenanthrene adsorption by soil. The adsorption of phenanthrene was significantly enhanced by the addition of EOMs, and the enhancement of distribution constant (Kd) was positively correlated with the content of soil organic Carbon (foc), indicating that the higher the soil foc, the more significant the promotion effect of EOMs addition on phenanthrene adsorption. On the contrary, the desorption of phenanthrene was obviously inhibited by the addition of EOMs. After 64 days of EOMs addition, the extractable amount of phenanthrene was decreased significantly, compared with the control. Since the organic matter content of peat was higher than that of commercial organic fertilizer, the decrease of extractable phenanthrene in soils added with peat was more significant. In addition, the higher the soil foc, the stronger inhibition effect of EOMs on extractability of phenanthrene. On the whole, exotic EOMs could promote the adsorption, while inhibit the desorption and reduce the extractability of phenanthrene in soils.

Mikrobiologiia. 2008 Mar-Apr; 77(2): 261-5
Pimenov NV, Ziakun AM, Prusakova TS, Lunina ON, Ivanov MV

The possibility of measuring the rates of light and dark CO2 assimilation using 13C Carbonate was demonstrated on Lake Kichier (Marii El). The application of methods utilizing the stable 13C and the radioactive 14C isotopes resulted in comparable values of the rates of light and dark CO2 fixation. Due to its absolute environmental safety, the method with 13C mineral Carbon can be recommended as an alternative to radioisotope methods for qualitative measurements of CO2 fixation rates in aquatic ecosystems.