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The Path of Carbon in Photosynthesis
Abstract
As knowledge regarding the formation of organic compounds from carbon dioxide and other inorganic materials in green plants accumulates, it becomes increasingly apparent that it is difficult to distinguish which transformations of carbon compounds should be classified as part of the pathway of carbon in photosynthesis and which reactions should be considered as other metabolic processes of the plant. All reactions of a photoautotrophic plant rely ultimately on the energy stored by the photosynthetic process. Therefore, any definition of carbon reduction during photosynthesis based on requirement of energy or equivalents of reducing agents should specify the requirement precisely. Even so, it is questionable whether such a definition can distinguish between carbon reduction reactions of photosynthesis and other metabolic transformations of carbon compounds. It is now believed that energy-carrying compounds such as adenosine triphosphate and reducing agents such as reduced triphosphopyridine nucleotide which are formed during respiratory processes may also be formed directly from products close to the primary photochemical reactions of photosynthesis. Transformations of carbon compounds which require such substances and which take place in the dark may also occur at a greatly accelerated rate during photosynthesis. Furthermore, most, if not all, of the reactions of carbon reduction in photosynthesis are known to occur, although at a diminished rate, in the dark long after the immediate reducing and energy-carrying agents formed from the photochemical reaction have decayed.
... Isotope tracer methods using radiocarbon ( 14 C) and/or stable carbon isotope ( 13 C) are essential for elucidating carbon fixation mechanisms because they can provide direct evidence for the presence of a specific pathway [8][9][10][11][12][13][14]. Barker and Kamen [15] performed the first 14 C-labeling experiment to determine the pathway of acetate formation by acetogens. ...
... vidually prepared: unlabeled formate (HCOOH),[1][2][3][4][5][6][7][8][9][10][11][12][13] C]formate (H 13 COOH), unlabeled acetate, [1-13 C]acetate, [2-13 C]acetate, and [U-13 C]acetate. Standard solution mixtures containing two or more isotopomers were prepared by mixing pure standards. ...
Anaerobic microbial acetogenesis is ubiquitous on Earth, and thus plays an important role in the global carbon cycle. The mechanism of carbon fixation in acetogens has attracted great interest from various studies for combatting climate change, and even for studying ancient metabolic pathways. Here, we developed a new, simple method for investigating carbon flows in the metabolic reaction of acetogen by conveniently and accurately determining the relative abundance of individual acetate- and/or formate-isotopomers formed in 13C labeling experiments. We measured the underivatized analyte by gas chromatography-mass spectrometry (GC-MS) coupled with a direct aqueous sample injection technique. The individual abundance of analyte isotopomers was calculated by the mass spectrum analysis using the least-squares approach. The validity of the method was demonstrated by determining known mixtures of unlabeled and 13C-labeled analytes. The developed method was applied to study the carbon fixation mechanism of the well-known acetogen Acetobacterium woodii grown on methanol and bicarbonate. We provided a quantitative reaction model for methanol metabolism of A. woodii, which indicated that methanol was not the sole carbon precursor of the acetate methyl group and that 20-22% of the methyl group was formed from CO2. In contrast, the carboxyl group of acetate appeared to form exclusively by CO2 fixation. Thus, our simple method, without laborious analytical procedures, has broad utility for the study of biochemical and chemical processes related to acetogenesis on Earth.
... This reaction produces two molecules of 3-phosphoglycerate. Molecules of 3-phosphoglycerate are further used to produce final organic compound such as sugar (Bassham and Calvin 1957). It is discovered by Melvin Calvin in 1940 (Vapaavuori 1986). ...
... In this pathway, ribulose 1, 5-bisphosphate carboxylase-oxygenase (RuBisCO) enzyme first catalyse the reaction in which CO 2 react with 5 Carbon sugar (ribulose 1, 5-bisphosphate; RuBP) and produce two molecules of 3-phosphoglycerate. Molecules of 3-phosphoglycerate are further used for sugar production (Bassham and Calvin 1957). Total 13 enzymes are involved in Calvin cycle, but RuBisCO is the key enzyme for CO 2 fixation (Fig. 1). ...
The increase in demand of fossil fuel uses for developmental activity and manufacturing of goods have resulted a huge emission of global warming gases (GWGs) in the atmosphere. Among all GWGs, CO2 is the major contributor that inevitably causes global warming and climate change. Mitigation strategies like biological CO2 capture through sequestration and their storage into biological organic form are used to minimize the concentration of atmospheric CO2 with the goal to control climate change. Since increasing atmospheric CO2 level supports microbial growth and productivity thus microbial-based CO2 sequestration has remarkable advantages as compared to plant-based sequestration. This review focuses on CO2 sequestration mechanism in bacteria through different carbon fixation pathways, involved enzymes, their role in calcite, and other environmentally friendly biomaterials such as biofuel, bioplastic, and biosurfactant.
Graphical abstract
... Among his many books, two are more familiar to most of us: Theory of Organic Chemistry (Branch and Calvin 1941) and The Path of Carbon in Photosynthesis (Bassham and Calvin 1957). With a nod toward the brand-new topic of radiation safety, Calvin assembled the first compendium of every synthesis with isotopic carbon, as well as, general principles for handling and measurement, into a guide for large-scale radiochemical and biological research (Calvin et al. 1949). ...
... For history and evolution of this area, see not only what Calvin (1989Calvin ( , 1992 wrote, but also what his two other major coworkers (Benson and Bassham) said (see: Bassham and Calvin 1957;Calvin and Bassham 1962;Benson 2002;Bassham 2003). Beautiful descriptions as well as photographs of Calvin may be viewed at the e-plaque at the California site (http://berke leypl aques .org/e-plaqu ...
Melvin Calvin (1911–1997) was the recipient of the 1961 Nobel Prize in Chemistry for the discovery of the canonical photosynthetic carbon reduction cycle. We present here a very brief glimpse of this extraordinary American scientist, who in his time was a preeminent force in physical and organic chemistry. Besides natural photosynthesis, Calvin’s prolific career included artificial photosynthesis, colors of organic substances, the origin of life, cancer, moon rocks, molecular basis of learning, and plant lipids & algal hydrocarbons as potential renewable sources of transport fuels.
... In these experiments, the exact position of the applied I3C-or "C-labe1 in the C-atoms of the final products squalene or cholesterol had been checked by a careful chemical degradation of these compounds. The Same techtuque of analyzing C-atom by C-atom had also been used at that time by Melvin Calvin and his group during the establishment of the photosynthetic carbon reduction cycle after application of '4C02 to green algae (Bassham and Calvin, 1957;Calvin, 1960). In fact, in the 1950s and beginning 1960s the time-consuming chemical degradation of the labeled organic compounds was the usual state-of-the-art in biosynthetic studies of most laboratories in order to find out the exact position of the applied carbon label. ...
... The recycling of chemical energy in reaction by-products to direct propagating supramolecular structures is a core feature in complex cellular networks. [1][2][3] The citric acid cycle in cells produces nucleotide phosphates such as NADH or guanosine-5'-triphosphate (GTP) as by-products when citrate undergoes backbone and functional group transformations into oxaloacetate. 4,5 These highenergy nucleotide phosphates promote, via covalent bond formation, the transformation of dormant molecules into active precursors that drive reversible superstructures of cytoskeletal polymers such as actin filaments and microtubules. ...
Structure formation in living systems builds upon balancing kinetic and thermodynamic landscapes powered by recycling covalent bond chemistry. Although recent synthetic efforts have been able to achieve these processes in part, the combination is necessary to identify key mechanisms that confer nature’s structural precision within a complex environment. We design a photolytic peptide that dissipates downstream chemical energy to control the transience and interconversion between its two active supramolecular forms via disulfide formation. The thiol assembles with slow kinetics via an isodesmic mechanism whereas the disulfide form induces aromatic chirality that propagates into helical twists within the nanostructure. Multiple structural states found under the same global conditions show that the assembly network demonstrate similar biological plasticity and can be directed by the recycling pathway. The approach demonstrate the importance of reaction complexity in creating supramolecular architectures that are inaccessible via conventional means.
... Plant photosynthesis is the basic ecological function and source of energy and food on Earth [46]. The specific life activities of green plants that absorb CO 2 and release oxygen (O 2 ) through photosynthesis provide important measures for the reduction in carbon emissions, thereby reducing the greenhouse effect to a certain extent [47]. Biofuels have a wide range of raw materials, such as cotton, peanuts, sunflowers, sugar cane and other plant materials [48]. ...
With the rapid development of the world economy, the demand for energy will inevitably increase the resource shortage and environmental pollution problems. Therefore, the coordinated development of energy and environment is an important way to achieve the United Nations (UN) Sustainable Development Goals (SDGs). Here, the dual biofuel intelligent charge compression ignition (ICCI) mode fuelled with butanol and biodiesel was demonstrated to achieve a high-efficiency and ultra-low emissions, which will have global real-world energy influence. The maximum thermal efficiency of the butanol/biodiesel ICCI mode is 3.5% higher than the absolute efficiency of the conventional mode, and the nitrogen oxide emissions decreased by 76.69% to 99.47%. The butanol/biodiesel ICCI mode has the potential to achieve carbon neutrality in the road transport sector and mitigate the greenhouse effect. Hence, direct air pollutants would be eliminated. Meanwhile, with the increasing production of biofuels worldwide, this work not only improves the environmental pollution and relieves the energy crisis, but also provides a method to deal with the mutual restraint between energy, environmental and technology.
... Limited studies have been reporting that short wave UV-C has a pronounced effect on plants' physiology and structure. It was reported that there induces a significant structural damaging effect on the plant cell, most specifically on the chloroplasts, mitochondria, and membranes [24,25]. The change in cellular structure is directly related to the overall alteration of the mechanical properties of the plant. ...
Amongst the surface treatment technologies to emerge in the last few decades, UV-C radiation surface treatment is widely used in food process industries for the purpose of shelf life elongation, bacterial inactivation, and stimulation. However, the short wave application is highly dose-dependent and induces different properties of the product during exposure. Mechanical properties of the agricultural products and their derivatives represent the key indicator of acceptability by the end-user. This paper surveys the recent findings of the influence of UV-C on the stress response and physiological change concerning the mechanical and textural properties of miscellaneous agricultural products with a specific focus on a potato tuber. This paper also reviewed the hormetic effect of UV-C triggered at a different classification of doses studied so far on the amount of phenolic content, antioxidants, and other chemicals responsible for the stimulation process. The combined technologies with UV-C for product quality improvement are also highlighted. The review work draws the current challenges as well as future perspectives. Moreover, a way forward in the key areas of improvement of UV-C treatment technologies is suggested that can induce a favorable stress, enabling the product to achieve self-defense mechanisms against wound, impact, and mechanical damage.
... The generated NADPH and ATP provide the energy required for CO2 fixation to generate the carbohydrates (8) in a process known as dark (light-independent) reactions or Calvin-Benson cycle 37,38 . ...
Bei der lichtinduzierten Oxidation von Wasser im Photosystem II (PSII) werden zwei wassermoleküle im katalytischen Zyklus des Metallclusters (Mn4CaO5) benötigt, und vier Protonen aus dem Cluster in den Lumen abgegeben. Daher ist es für das Verständnis des Mechanismus´ der Wasseroxidation von entscheidender Bedeutung, die Veränderung der Protonierungszustände am cluster während der Katalyse zu untersuchen. Hierbei sollten sowohl die Wasserkanäle für die Zuführung der Substratwassermoleküle als auch die Transportwege für die Freisetzung der Protonen untersucht werden. Deshalb wurde in meiner ersten Veröffentlichung ein neues Protokoll entwickelt, um einzelne große Kristalle von dPSII mit einer Länge von ~3 mm in der Längsachse zu züchten. Diese Kristalle mit einer Auflösung von ca. 8 Å gemessen. Um eine höhere Auflösung zu erzielen, ist die Verbesserung der Kristallqualität essenziell. Daher wurde in meiner zweiten Veröffentlichung die Struktur des Detergens-Protein-Komplexes von dPSII mit βDM, durch Anwendung von SANS in Kombination mit SAXS untersucht. Die Ergebnisse zeigten, dass βDM eine monomolekulare Schicht um dPSII bildet. Darüber hinaus konnten freie Mizellen von βDM in der Lösung nachgewiesen werden. Damit ist eine weitere Optimierung der βDM-Konzentration in der Proteinlösung erforderlich, um die Bildung von freien Mizellen zu minimieren. In meiner dritten Veröffentlichung wurde die strukturelle Dynamik in den Wasserkanälen, während des S2-S3 Übergangs mit Hilfe der XFEL untersucht. Ein Datensatz mit einer hohen Auflösung von 1,89 Å wurde durch die Zusammenführung von Daten gewonnen, die während des S2-S3 Übergangs gesammelt wurden. In Anbetracht der Analyse der zusammengeführten Daten und der einzelnen Zeitpunkte, die während des S2-S3 Übergangs gesammelt wurden, ist es wahrscheinlich, dass ein Substratwasser durch den O1-Kanal geliefert wird. Im Gegensatz dazu wird ein Proton aus dem Cluster durch den Cl1 Transportweg in Richtung Lumen freigesetzt.
... [22,23] Both components are required to reduce carbon dioxide in a light-independent multi-step process known as Calvin cycle. [24] Figure 3. Graphical illustration of photosynthetic processes with light and dark reactions for the conversion of water and carbon dioxide to molecular oxygen and carbohydrates, respectively. ...
In light of the rapidly increasing global demand of energy and the negative effects of climate change, innovative solutions that allow an efficient transition to a carbon-neutral economy are urgently needed. In this context, artificial photosynthesis is emerging as a promising technology to enable the storage of the fluctuating energy of sunlight in chemical bonds of transportable “solar fuels”. Thus, in recent years much efforts have been devoted to the development of robust water oxidation catalysts (WOCs) leading to the discovery of the highly reactive Ru(bda) (bda: 2,2’-bipyridine-6,6’-dicarboxylic acid) catalyst family. The aim of this thesis was the study of chemical and photocatalytic water oxidation with functionalized Ruthenium macrocycles to explore the impact of substituents on molecular properties and catalytic activities of trinuclear macrocyclic Ru(bda) catalysts. A further objective of this thesis comprises the elucidation of factors that influence the light-driven water oxidation process with this novel class of supramolecular WOCs.
... Photosynthetic growth occurs via the conversion of molecular excitations into long-lived chemical energy in the form of adenosine triphosphate (ATP) and reduced nicotinamide adenine dinucleotide phosphate. These energy-rich molecules fuel the fixation of CO2 via the Calvin-Benson-Bassham cycle [112]. The overall process of photosynthesis is fairly thermodynamically inefficient, with a practical maximal efficiency of light to biomass conversion of below 10% [113,114]. ...
Understanding the rules of life is one of the most important scientific endeavours and has revolutionised both biology and biotechnology. Remarkable advances in observation techniques allow us to investigate a broad range of complex and dynamic biological processes in which living systems could exploit quantum behaviour to enhance and regulate biological functions. Recent evidence suggests that these non-trivial quantum mechanical effects may play a crucial role in maintaining the non-equilibrium state of biomolecular systems. Quantum biology is the study of such quantum aspects of living systems. In this review, we summarise the latest progress in quantum biology, including the areas of enzyme-catalysed reactions, photosynthesis, spin-dependent reactions, DNA, fluorescent proteins, and ion channels. Many of these results are expected to be fundamental building blocks towards understanding the rules of life.
... C 3 plants fix carbon through the Benson-Calvin cycle initiated by the reduction of ribulose-1,5-bisphosphate to the 3-carbon compound, 3-phosphoglycerate, via the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). 43,44 RuBisCO highly discriminates against 13 CO 2 , resulting in the relatively low d 13 C values measured from C 3 plants. 45 On the basis of bulk carbon analysis of plant material, d 13 C values of C 3 plants range from -32 to -20 mUr (average, -27 mUr). ...
Due to differences in carbon assimilation pathways between plants, there are subtle but distinct variations in the carbon isotope ratios of foods and animal products throughout the food supply. Although it is well understood that the carbon isotope ratio composition of the diet influences that of the consumers' tissues, the application of natural abundance carbon isotope ratio analysis in nutrition has long been underappreciated. Over the past decade, however, several studies have investigated the utility of carbon isotope ratio analysis for evaluation of nutritional biomarker status, primarily focusing on its application as an objective indicator of sugar and animal protein intake. More recently, research investigating the application of natural abundance measurements has been extended to study fatty acid metabolism and has yielded encouraging results. Collectively, data from large-scale observational studies and experimental animal studies highlight the potential for carbon isotope ratio analysis as an additional and effective tool to study diet and metabolism. The purpose of this review is to provide an overview of natural abundance carbon isotope ratio analysis, its application to studying nutrition, and an update of the research in the field.
... metabolic processes, in particular the fixation of carbon dioxide (CO 2 ) through the Calvin-Benson-Bassham (CBB) cycle (1). ...
Hybrid approach catches light
Plant chloroplasts enclose two major photosynthetic processes: light reactions, which generate the energy carriers adenosine triphosphate and reduced nicotinamide dinucleotide phosphate (NADPH), and dark reactions, which use these molecules to fix carbon dioxide and build biomass. Miller et al. appropriated natural components, thylakoid membranes from spinach, for the light reactions and showed that these could be coupled to a synthetic enzymatic cycle that fixes carbon dioxide within water-in-oil droplets. The composition of the droplets could be tuned and optimized and the metabolic activity monitored in real time by NADPH fluorescence (see the Perspective by Gaut and Adamala). These chloroplast-mimicking droplets bring together natural and synthetic components in a small space and are amenable to further functionalization to perform complex biosynthetic tasks.
Science , this issue p. 649 ; see also p. 587
... These ideas were further developed in 25 and later investigated in [26][27][28] , and were tested experimentally 29 . Other famous examples of self-sustaining cycles include the autocatalytic Bethe-Weizsäcker cycle of hydrogen burning in the sun 30 , or the Calvin cycle 31 of photosynthesis in plants. The interaction structure of complex systems often evolves over time (co-evolution), and cycles may get created and destroyed in this process. ...
The collapse of ecosystems, the extinction of species, and the breakdown of economic and financial networks usually hinges on topological properties of the underlying networks, such as the existence of self-sustaining (or autocatalytic) feedback cycles. Such collapses can be understood as a massive change of network topology, usually accompanied by the extinction of a macroscopic fraction of nodes and links. it is often related to the breakdown of the last relevant directed catalytic cycle within a dynamical system. Without detailed structural information it seems impossible to state, whether a network is robust or if it is likely to collapse in the near future. Here we show that it is nevertheless possible to predict collapse for a large class of systems that are governed by a linear (or linearized) dynamics. to compute the corresponding early warning signal, we require only non-structural information about the nodes' states such as species abundances in ecosystems, or company revenues in economic networks. It is shown that the existence of a single directed cycle in the network can be detected by a "quantization effect" of node states, that exists as a direct consequence of a corollary of the Perron-Frobenius theorem. the proposed early warning signal for the collapse of networked systems captures their structural instability without relying on structural information. We illustrate the validity of the approach in a transparent model of co-evolutionary ecosystems and show this quantization in systems of species evolution, epidemiology, and population dynamics.
... The CBC is subdivided into three stages, carboxylation, reduction and regeneration. The cycle, elucidated by Melvin Calvin et al in the 1950s [25,26], involves 11 enzymes, which catalyse 13 different steps (Figure 1). Transgenic studies have demonstrated any decrease in any one of the key enzymes of the CBC has a significant negative impact on the rate of carbon assimilation and plant growth. ...
Increasing demands for food and resources are challenging existing markets, driving a need to continually investigate and establish crop varieties with improved yields and health benefits. By the later part of the century, current estimates indicate that a >50% increase in the yield of most of the important food crops including wheat, rice and barley will be needed to maintain food supplies and improve nutritional quality to tackle what has become known as ‘hidden hunger’. Improving the nutritional quality of crops has become a target for providing the micronutrients required in remote communities where dietary variation is often limited. A number of methods to achieve this have been investigated over recent years, from improving photosynthesis through genetic engineering, to breeding new higher yielding varieties. Recent research has shown that growing plants under elevated [CO2] can lead to an increase in Vitamin C due to changes in gene expression, demonstrating one potential route for plant biofortification. In this review, we discuss the current research being undertaken to improve photosynthesis and biofortify key crops to secure future food supplies and the potential links between improved photosynthesis and nutritional quality.
... Photosynthesis in leaves is a well-established and extremely well researched process whereby plants harvest the energy from sunlight and use this to convert CO 2 into soluble carbohydrates, which are subsequently used for plant growth (Calvin and Benson, 1948;Bassham and Calvin, 1960;Raines, 2003;Biel and Fomina, 2015). Photosynthesis is responsible, therefore, either directly (through plant growth) or indirectly (through the food chain), for all food consumed worldwide. ...
Photosynthesis is currently a focus for crop improvement, however the majority of this work has taken place and been assessed in leaves, whilst limited consideration has been given to the contribution that other green tissues make to whole plant carbon assimilation. The major focus of this review is to evaluate the impact of non-foliar photosynthesis on carbon use efficiency and total assimilation. Here we appraise and summarise past and current literature on the substantial contribution of different photosynthetically active organs and tissues to productivity in a variety of different plant types, with an emphasis on fruit and cereal crops. Previous studies provide evidence that non-leaf photosynthesis could be an unexploited potential target for crop improvement. We also briefly examine the role of stomata in non-foliar tissues and their role in gas exchange, maintenance of optimal temperatures and thus photosynthesis. In the final section, we discuss possible opportunities to manipulate these processes and provide evidence that wheat plants genetically manipulated to increase leaf photosynthesis, also displayed higher rates of ear assimilation, which translated to increased grain yield. By understanding these processes, we can start to provide insights into manipulating non-foliar photosynthesis and stomatal behaviour to identify novel targets for exploitation for on-going breeding programmes.
... Powered by sunlight, PS-II extracts electrons from water producing oxygen, while PS-I uses light to reduce NADP + to NADPH. Electron transfer from PS-II to PS-I is coupled to proton transfer and used to form ATP. The final product of the Calvin cycle [16] using both NADPH and ATP is a reduced sugar. ...
Quantum biology is the application of the theory of open quantum systems to aspects of biology where classical physics fails to give an accurate de- scription. The most well-established area in quantum biology is the study of photosynthesis.
There exists a body of evidence that the primary photosynthetic processes of energy and charge transfer exhibit quantum mechanical properties essential for function and that cannot be described by classical physics. Open quantum systems models of excitation energy transfer and electron transfer in primary photosynthesis have elucidated many aspects of the relation between struc- ture and function in the photosynthetic complex, as well as contributed to an understanding of the role of the environment in quantum transport processes.
After an introduction to quantum biology, an overview of open quantum systems approaches to transfer processes in primary photosynthesis is given. Our results on decoherence-assisted transport in the context of photosyn- thetic excitation energy transfer, as well as our proposal of the direct role of spin in a protection mechanism during photosynthetic charge transfer, are presented. Finally, thoughts around an outlook for quantum biology are given.
... Finally, the NADPH and the ATP are utilized for the construction of carbohydrates by reduction of CO2 in a series of dark reactions described by the Calvin cycle. [100] The holes which are accumulated during this entire process at the oxygen evolving cluster become filled with electrons obtained from water oxidation. Consequently, each absorbed photon leads to the extraction of one electron from a water molecule. ...
The catalytic splitting of water into its elements is an important reaction to establish hydrogen as a solar fuel. The bottle-neck of this process is considered to be the oxidative half reaction generating oxygen, and good catalysts are required to handle the complicated redox chemistry involved. As can be learned from nature, the incorporation of the catalytically active species into an appropriate matrix can help to improve the overall performance. Thus, the aim of the present thesis was to establish novel supramolecular approaches to improve water oxidation catalysis using the catalytically active {Ru(bda)} fragment as key motive (bda = 2,2'-bipyridine-6,6'-dicarboxylate). First, the synthesis of ruthenium catalysts gathering three {Ru(bda)} water oxidation subunits in a macrocyclic fashion is described. By using bridging bipyridine ligands of different lengths, metallosupramolecular macrocycles with distinct sizes have been obtained. Interestingly, an intermediate ring size has been proven to be optimal for the catalytic water oxidation. Detailed kinetic, spectroscopic, and theoretical studies helped to identify the reaction mechanism and to rationalize the different catalytic activities. Furthermore, solubilizing side chains have been introduced for the most active derivative to achieve full water solubility. Secondly, the {Ru(bda)} fragment was embedded into supramolecular aggregates to generate more stable catalytic systems compared to a homogeneous reference complex. Therefore, the catalyst fragment was equipped with axial perylene bisimide (PBI) ligands, which facilitate self-assembly. Moreover, the influence of the different accessible aggregate morphologies on the catalytic performance has been investigated.
Biogas, generated through anaerobic digestion (AD) of organic feed-stocks like bio-wastes, is a sustainable and clean source of energy, capable of generating electricity, and direct thermal use. However, biogas is a mixture of methane and CO2 and the latter does not contribute towards the overall heating value of the gaseous fuel. The AD process also generates digestate slurry which is generally rich in ammonia-based nitrogen, phosphorous, and potassium (NPK). While the solid part of the effluent is traditionally utilized as fertilizers, the liquid digestate requires proper treatment and management to prevent leach out and contamination of the ground water systems. Algal cultivation (AC), on the other hand, is gaining attention for CO2 capture and for the generation of algal lipids and biochemicals, like proteins, carbohydrates, and pigments. Algal cultivation systems can be integrated as photo bioreactors for CO2 scrubbing in a two stage system or as anaerobic membrane reactors combining AD and algal processes along with membrane filtration technology for enhancing nutrient recovery, Therefore, algal cultivation can act as a potential CO2 trap for upgradation of the quality of biogas by enhancing methane concentration while utilizing the nutrient (NPK) rich effluent from AD process. The algal biomass can be further processed for the production of value-added biochemicals and bioenergy applications, like biodiesel production. The present article focuses on the prospects and challenges of the integration of AD and AC processes which can have potential implications on bioenergy sector.
Isotope technology is an important means to trace the source of substances. Isotope technology plays an important role in the study of the process and mechanism of photosynthetic oxygen evolution and photosynthetic assimilation. This chapter introduces the process by which scientists discovered several photosynthetic pathways using 14C labels. The experiment of 18O tracing photosynthetic oxygen evolution is summarized, the photosynthetic oxygen evolution only from water was debated and questioned, and it was concluded that the oxygen released by photosynthesis comes not only from water photolysis but also from bicarbonate photolysis. A reasonable explanation of the Dole effect is given according to the photosynthetic oxygen evolution equally from bicarbonate and water. Meanwhile, this chapter also explained why the δ18O of cellulose in tree rings can trace the paleoclimatic environment, although it has little relationship with the source water. Due to the strong isotopic exchange and fractionation, it is difficult to quantitatively distinguish the utilization of root-derived bicarbonate and carbon dioxide from the atmosphere by traditional isotope techniques. This chapter focuses on the principle and technical essentials of bidirectional isotope tracing culture technology. The inorganic carbon sources and utilization pathways of microalgae were described, and the determination methods of direct carbon sinks and indirect carbon sinks of plants were proposed. This chapter describes in detail the measurement of the rate of bicarbonate uptake by plants, the average stable carbon isotopic composition of atmospheric carbon dioxide, the ability of root-derived bicarbonate use by plants and the total photosynthetic capacity by means of bidirectional isotope tracing culture technology. Finally, this chapter also introduced the method of quantitative determination of bicarbonate utilization capacity of wild plants and discussed the metabolic diversity characteristics of karst-adaptable plants. Quantitative determination of the root-derived bicarbonate use capacity of plants provides a scientific basis for the scientific assessment of productivity in karst areas, accurate measurement of karst carbon sinks, and screening of karst-adaptable plants.KeywordsIsotope technologyBidirectional isotope tracing cultureInorganic carbon assimilationInorganic carbon utilization pathwayDole effectIndirect carbon sinkRoot-derived bicarbonate
The lightening of structures is a constant preoccupation of the mobility industries and particularly the automotive industry. For vehicles with thermal propulsion, this quest for lightening is justified by the need to reduce fossil fuel consumption, and consequently the emissions of CO2 and harmful particles. The increase in the amount of CO2 in the world has greatly disturbed the functioning of the earth. Important projects are being implemented worldwide to reduce the emissions of this gas, but no solution has yet been adopted and no strategy is currently recognized. To cope with this increase of CO2 in our environment, effective and reliable carbon sequestration technologies are urgently needed. Biological CO2 sequestration using algae is currently one of the most efficient and cost-effective of the various CO2 sequestration methods. Indeed, algae are widely exploitable as a CO2 storage medium and can be used to produce biofuels and many value-added products. In this study, we review the state of recent research on the use of microalgae in CO2 sequestration.
This article presents perennial grasses, without whose presence it is impossible to imagine the natural environment as well as agriculture, recreation, sport, and satisfactory aesthetics of the environment. Grasses have by far the widest distribution of all flowering families, grow on every continent, and are part of all the major biomes of the terrestrial world. They not only occur in almost all types of natural landscapes but also find a prominent place in the agricultural landscape. Grasses are not only a source of food for people (wheat, rice, maize, millet, etc.) and feed for livestock, but also a source of energy, building materials, a component of paper pulp, etc. Moreover, grasses have numerous uses to enhance the beauty of the surrounding landscape, bring relaxation, health, and comfort to people (i.e., gardens, parks, and sports facilities), and support land protection. This article describes just these, not often mentioned, and characterized grass uses, with an emphasis on the relationship between different species of perennial grasses and their functionality. The aim is to show the various aspects of the amenity use of grasses in the context of species diversity and their future under the conditions of a changing climate.
Glaucous (811, L35, and RXL10) and non-glaucous (811bw, L35bw, and RXL10bw) near-isogenic lines (NILs) of rye ( Secale cereale L.) forming three pairs of inbred lines were the subject of the research. The research aimed to study the relationship between wax cover attributes and the physio-biochemical drought reactions and yield of rye NILs and to uncover the differences in drought resistance levels of these lines. The greatest differences between glaucous and non-glaucous NILs were observed in the RXL10/RXL10bw pair. Of particular note were the stable grain number and the thousand grain weight of the non-glaucous line RXL10bw under drought and the accompanying reactions, such as an approximately 60% increase in MDA and a two-fold increase in wax amount, both of which were significantly higher than in the glaucous line RXL10 and in other NILs. The surprisingly high level of MDA in the RXL10bw line requires further analysis. Moreover, additional wax crystal aggregates were found under drought conditions on the abaxial leaf surface of the glaucous lines 811 and RXL10. The use of rye NILs indicated that line-specific drought resistance could be associated with wax biosynthetic pathways involved in physiological and biochemical responses important for increased drought resistance.
Artículo dedicado a la memoria de Melvin Calvin, premio Nobel de química en 1961, con ocasión del primer centenario de su nacimiento (2011)
Malic acid is a component of the rhizosphere exudate and is vital for crop growth. However, little information is available about the effects of external applications of malic acid on the nutrient absorption and quality of grape fruit, and few studies have been performed on the relationship between the changes in the rhizosphere microbial community and nutrient absorption and fruit quality of grapes after adding malic acid. Here, the LM (low concentration of malic acid) and HM (high concentration of malic acid) treatments comprised 5% and 10% malic acid (the ratio of acid to the total weight of the fertilizer) combined with NPK fertilizer, respectively. Applying malic acid changed the grape rhizosphere microbial community structure and community-level physiological profile (CLPP) significantly, and HM had a positive effect on the utilization of substrates. The microbial community structure in the rhizosphere of the grapes with added malic acid was closely related to the CLPP. The N and P content in the leaves and fruits increased after applying malic acid compared to the control, while K content in the fruits increased significantly. In addition, malic acid significantly reduced the weight per fruit, significantly increased soluble sugar content (SSC) and vitamin C content of the fruit, and significantly improved the fruit sugar-acid ratio and grape tasting score. Moreover, the principal component analysis and grape nutrient and fruit quality scores showed that grape nutrients and fruit quality were significantly affected by malic acid and ranked as 5% malic acid > 10% malic acid > control. Pearson’s correlation heatmap of microbial composition, nutrient absorption and fruit quality of the grapes showed that the grape microbial community was closely related to grape nutrients and fruit quality. Adding malic acid was positively correlated to Planococcaceae, Bacillaceae, Woeseiaceae and Rhodobacteraceae. Furthermore, Planococcaceae, Bacillaceae, Woeseiaceae and Rhodobacteraceae were closely related to grape nutrient absorption and fruit quality. Bacillaceae and Woeseiaceae were positively correlated with total soluble sugar, while Planococcaceae and Rhodobacteraceae were positively correlated with titratable acid. Hence, Bacillaceae and Woeseiaceae were the key bacteria that played a major role in grape fruit quality and nutrient absorption after applying malic acid water-soluble fertilizer.
Diatoms are unicellular algae that perform photosynthesis, a process that comprises both the electron transport processes in the thylakoid membranes and the reactions involved in CO2 fixation. The latter process is the starting point for carbohydrate biosynthesis and numerous reactions and pathways in different cellular locations, including the generation, modification, conversion, subsequent storage, and degradation of carbohydrates. While there is vast knowledge of these processes available of land plants and green algae, much less is known of algae like diatoms that are derived from secondary endosymbiosis. Comparative studies on the localization and regulation of photosynthetic pathways in recent years revealed in principle a similarity of photosynthesis in land plants and diatoms, but also a number of peculiar differences, which may be due both to the general phylogenetic distance between these groups and the evolution of diatoms by secondary endosymbiosis, resulting in a different genetic background. This chapter describes the current knowledge of CO2 acquisition and fixation processes in diatoms on the molecular, cellular, and physiological levels in diatoms. Additional focus is laid on photorespiration, as well as carbohydrate pathways, carbohydrate degradation, and carbohydrate storage.
Upregulation of triacylglycerols (TAGs) in vegetative plant tissues such as leaves has the potential to drastically increase the energy density and biomass yield of bioenergy crops. In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. Here we present a core metabolism model for the C4 biomass crop Sorghum bicolor (iTJC1414) along with a minimal model for photosynthetic CO2 assimilation, sucrose and TAG biosynthesis in C3 plants. Extending iTJC1414 to a four-cell diel model we simulate C4 photosynthesis in mature leaves with the principal photo-assimilatory product being replaced by TAG produced at different levels. Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. For plant generic pathways, ATP- and NADPH-demands per CO2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the photosynthetic supply in ATP and NADPH in iTJC1414 is adjusted to be balanced for sucrose as the sole photo-assimilatory product, overproduction of TAG is predicted to cause a substantial surplus in photosynthetic ATP. This means that if TAG synthesis was the sole photo-assimilatory process, there could be an energy imbalance that might impede the process. Adjusting iTJC1414 to a photo-assimilatory rate that approximates field conditions, we predict possible daily rates of TAG accumulation, dependent on varying ratios of carbon partitioning between exported assimilates and accumulated oil droplets (TAG, oleosin) and in dependence of activation of futile cycles of TAG synthesis and degradation. We find that, based on the capacity of leaves for photosynthetic synthesis of exported assimilates, mature leaves should be able to reach a 20% level of TAG per dry weight within one month if only 5% of the photosynthetic net assimilation can be allocated into oil droplets. From this we conclude that high TAG levels should be achievable if TAG synthesis is induced only during a final phase of the plant life cycle.
Photosynthetic pigments are an integral and vital part of all photosynthetic machinery and are present in different types and abundances throughout the photosynthetic apparatus. Chlorophyll, carotenoids and phycobilins are the prime photosynthetic pigments which facilitate efficient light absorption in plants, algae, and cyanobacteria. The chlorophyll family plays a vital role in light harvesting by absorbing light at different wavelengths and allowing photosynthetic organisms to adapt to different environments, either in the long-term or during transient changes in light. Carotenoids play diverse roles in photosynthesis, including light capture and as crucial antioxidants to reduce photodamage and photoinhibition. In the marine habitat, phycobilins capture a wide spectrum of light and have allowed cyanobacteria and red algae to colonise deep waters where other frequencies of light are attenuated by the water column. In this review, we discuss the potential strategies that photosynthetic pigments provide, coupled with development of molecular biological techniques, to improve crop yields through enhanced light harvesting, increased photoprotection and improved photosynthetic efficiency.
With thousands of discovered planets orbiting other stars and new missions that will explore our solar system, the search for life in the universe has entered a new era. However, a reference database to enable our search for life on the surface of icy exoplanets and exomoons by using records from Earth's icy biota is missing. Therefore, we developed a spectra catalogue of life in ice to facilitate the search for extraterrestrial signs of life. We measured the reflection spectra of 80 microorganisms-with a wide range of pigments-isolated from ice and water. We show that carotenoid signatures are wide-ranged and intriguing signs of life. Our measurements allow for the identification of such surface life on icy extraterrestrial environments in preparation for observations with the upcoming ground- and space-based telescopes. Dried samples reveal even higher reflectance, which suggests that signatures of surface biota could be more intense on exoplanets and moons that are drier than Earth or on environments like Titan where potential life-forms may use a different solvent. Our spectra library covers the visible to near-infrared and is available online. It provides a guide for the search for surface life on icy worlds based on biota from Earth's icy environments.
Carbon dioxide containing waste gasses from combustion processes as well as organically loaded wastewaters are anthropogenic waste streams that are the cause of significant environmental degradation. Research into the use of microalgae to valorize these streams to valuable energy and chemical products is gaining momentum.
This chapter aims to present the current stage of knowledge in the field of phycovalorization of these waste streams to biodiesel; biodiesel from microalgae is classified as a third-generation biofuel. The chapter considers the carbon sequestration of waste gasses to algal biomass, treatment of organic wastewater to algal biomass, the current knowledge and potential limitations of simultaneous carbon (mixotrophic) phycoremediation of waste gas and organic wastewater to algal biomass, and the ultimate conversion of algal biomass to biodiesel. In addition, the chapter presents potential reactor configurations currently under investigation with the potential for commercial scale-up and considerations in term of algal strain selection required to ensure commercial success of these phycovalorization processes.
Research on microbial diversity, interaction between microbes and soil physiochemical properties, role of microbes in biogeochemical cycles, and climate change have guided the scientific community to understand the soil and environmental health. Carbon is one of the essential elements of the soil, oceans, atmosphere, crustal rocks, kerogen (solid hydrocarbon for the formation of fuels), and reserve in various forms called carbon sink. Carbon-containing organic molecules flux between all these ecosystems (reservoirs) for the balance and sustainable function of the ecosystems via active carbon cycle. Carbon is the prime element for building a life on Earth which is fixed in various forms in the terrestrial and marine plants through photosynthesis. Microorganisms play regulatory role in biogeochemical cycles and shaping any kind of ecosystems. There are huge diversity of soil and aquatic microbes like Acetobacterium woodii, Aquifex aeolicus, Archaebacteria brierleyi, Ignicoccus hospitalis, Chlorobium limicola, C. tepidum, C. thiosulfatophilum, C. phaeobacteroides, Chloroflexus aurantiacus, C. aggregans, Chromatium vinosum, Clostridium thermoaceticum, Crenarchaeota, Desulfobacter hydrogenophilus, Desulfurobacterium crinifex, D. thermolithotrophum, Halobacterium salinarum, Thiobacillus ferrooxidans, Hydrogenobacter hydrogenophilus, H. thermophilus, Metallosphaera sedula, Moorella thermoacetica, Pyrobaculum aerophilum, Pyrobaculum islandicum, Pyrolobus fumarii, Rhodobacter sphaeroides, Rhodopseudomonas viridis, Rhodospirillum rubrum, Stygiolobusa zoricus, Sulfolobus metallicus, Sulfurihydrogenibium subterraneum, Thermocrinis ruber, Thermoproteus neutrophilus, Thermovibrio ammonificans, T. ruber, and Thiomicrospira denitrificans, and also order Rhizobiales are able to fix the various forms of carbon through numerous pathways such as Calvin cycle, reductive acetyl-coenzyme A pathway, reductive citric acid cycle, dicarboxylate/4-hydroxybutyrate cycle (DC/HB), hydroxypropionate/4-hydroxybutyrate cycle (HP/HB), and 3-hydroxypropionate bicycle. The fixed carbon is used by these microbes for their growth and development and also to make it available for other organisms. The carbon sequestration efficiency of plants and microbes by biotic (photosynthesis and respiration) processes plays key crucial role in mitigation of global climate change and environmental stability. In spite of the use of modern biotechnologies in research, huge information of microbial diversity and role in balancing of biogeochemical cycle are still not fully known. Therefore, it is crucial to discuss in-depth the scientific knowledge of microbial carbon fixation processes and its role in the mitigation of global climate change in present era.
Knowledge of the genetic basis for autotrophic metabolism is valuable since it relates to both the emergence of life and to the metabolic engineering challenge of incorporating CO2 as a potential substrate for biorefining. The most common CO2 fixation pathway is the Calvin cycle, which utilizes Rubisco and phosphoribulokinase enzymes. We searched thousands of microbial genomes and found that 6.0% contained the Calvin cycle. We then contrasted the genomes of Calvin cycle-positive, non-cyanobacterial microbes and their closest relatives by enrichment analysis, ancestral character estimation, and random forest machine learning, to explore genetic adaptations associated with acquisition of the Calvin cycle. The Calvin cycle overlaps with the pentose phosphate pathway and glycolysis, and we could confirm positive associations with fructose-1,6-bisphosphatase, aldolase, and transketolase, constituting a conserved operon, as well as ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and phosphoglycerate kinase. Additionally, carbohydrate storage enzymes, carboxysome proteins (that raise CO2 concentration around Rubisco), and Rubisco activases CbbQ and CbbX accompanied the Calvin cycle. Photorespiration did not appear to be adapted specifically for the Calvin cycle in the non-cyanobacterial microbes under study. Our results suggest that chemoautotrophy in Calvin cycle-positive organisms was commonly enabled by hydrogenase, and less commonly ammonia monooxygenase (nitrification). The enrichment of specific DNA-binding domains indicated Calvin-cycle associated genetic regulation. Metabolic regulatory adaptations were illustrated by negative correlation to AraC and the enzyme arabinose-5-phosphate isomerase, which suggests a downregulation of the metabolite arabinose-5-phosphate, which may interfere with the Calvin cycle through enzyme inhibition and substrate competition. Certain domains of unknown function that were found to be important in the analysis may indicate yet unknown regulatory mechanisms in Calvin cycle-utilizing microbes. Our gene ranking provides targets for experiments seeking to improve CO2 fixation, or engineer novel CO2-fixing organisms.
This thesis reports studies of the components of the electron acceptor complex of photosystem II isolated from the thermophilic cyanobacterium Phormidium laminosum. The principal technique used has been electron paramagnetic resonance spectrometry (epr): epr signals are characterised by lineshape and g-value. This thesis reports the first detection of the g = 1.9 signal (assigned to the interaction Qa Fe2+) by photoreduction at 77K of Qa in PS II from P. laminosum. This signal could be replaced by the g = 1.8 signal by treatment with formate, an inhibitor of electron transfer between the two quinones, which displaces bicarbonate from its ligation site at the non-heme iron. A third signal, with g ≈ 1.6 was detected and assigned as described below. Using epr signals, the midpoint potential of Qa/Qa was measured with either bicarbonate or formate bound to the iron. At pH 7.8, both were found to have midpoint potentials of ≈ +25mV. This represented the first direct determination of the redox potential of Qa in the presence of bicarbonate, and suggested that formate does not inhibit simply by affecting the redox potential of Qa. Unlike titrations of in higher plant PS II, there was no indication of further low-potential quinone acceptors. However, the behaviour of a signal due to the interaction of the iron-semiquinone and photoreduced pheophytin indicated some involvement of another electron acceptor, with midpoint potential of -250mV. These results were supported by kinetic optical spectrophotometry. The assignment of the epr signal with g ≈ 1.6 to an interaction of Qa -Fe2+ with Qb- was made. Using this signal, a direct estimate of the midpoint potential for the couple in PS II (≈ +60mV) was made; evidence was found also for pH- dependence of the signal which indicated the possible second reduction of at around this potential. It was found that the g ≈ 1.6 can be either 77K or 200K photoinduced following saturating illumination at room temperature, indicating the dark stability of the Qb- species, . Applying this protocol, an epr signal due to -Fe2+ was proposed; and interactions of a (phenyl- para-benzoquinone) with the non-heme iron could be monitored. Similar signals are seen following 77K illumination of both cyanobacterial and spinach PS II treated with the analogue, tribromotoluquinone. The technique extended X-ray absorption fine-structure (EXAFS) was used to probe of the structure of the manganese complex of PS II from spinach. The results were consistent with an arrangement of the four manganese of the oxygen-evolving complex either as two μ-oxo bridged dimers, or a μ-oxo-bridged trimer with a single monomeric manganese.
Inorganic carbon fixation is the most important biosynthetic process on Earth and the oldest type of metabolism. The autotrophic HP/HB cycle functions in
CrenarchaeaSulfolobalesArchaeaThaumarchaeota
Spinach leaf ribulose 1,5-diphosphate carboxylase is reversibly inhibited by cyanide at low concentration; 10⁻⁵M and 10⁻⁴M cyanide inhibit the carboxylation reaction 51% and 91%, respectively. Inhibition by cyanide (Ki = 1.6 × 10⁻⁵M) is uncompetitive (anticompetitive) with respect to ribulose 1,5-diphosphate (ribulose-1,5-di-P) and is of mixed character with respect to Mg²⁺ and HCO3⁻. This and other kinetic evidence suggest that cyanide combines readily with enzyme-ribulose-1,5-di-P complex, but not with enzyme.
The inference that enzyme-ribulose-1,5-di-P complex reacts with cyanide to form an inactive ternary complex is supported by binding studies with the use of the gel filtration technique. Ribulose-1,5-di-P uniformly labeled with ¹⁴C is tightly bound to the carboxylase (1.04 moles of ribulose-1,5-di-P per mole of enzyme) only in the presence of cyanide and ¹⁴C-cyanide is bound to the carboxylase (1.06 moles of cyanide per mole of enzyme) only in the presence of ribulose-1,5-di-P. The presence of Mg²⁺ is without effect on ¹⁴C-ribulose-1,5-di-P binding in the presence of cyanide or on ¹⁴C-cyanide binding in the presence of ribulose-1,5-di-P under the conditions used. A ternary complex of ribulose-1,5-di-P carboxylase, ribulose-1,5-di-P, and cyanide in a mole ratio of 1:1:1 is indicated. Attempts to demonstrate Schiff base formation between the carboxylase and ribulose-1,5-di-P under a wide variety of conditions were unsuccessful.
Photosynthetic organisms are essential for human life, yet most of their genes remain functionally uncharacterized. Single-celled photosynthetic model systems have the potential to accelerate our ability to connect genes to functions. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. 78% of genes are represented by at least one mutant that showed a phenotype, providing clues to the functions of thousands of genes. Mutant phenotypic profiles allow us to place known and previously uncharacterized genes into functional pathways such as DNA repair, photosynthesis, the CO2-concentrating mechanism, and ciliogenesis. We illustrate the value of this resource by validating novel phenotypes and gene functions, including the discovery of three novel components of a defense pathway that counteracts actin cytoskeleton inhibitors released by other organisms. The data also inform phenotype discovery in land plants: mutants in Arabidopsis thaliana genes exhibit similar phenotypes to those we observed in their Chlamydomonas homologs. We anticipate that this resource will guide the functional characterization of genes across the tree of life.
Carboxysomes are a group of bacterial microcompartments (BMCs) that encapsulate Rubisco and carbonic anhydrase to enhance CO2 fixation in cells. Through self-assembly of hundreds of proteins into a virus-like icosahedral organelle, carboxysomes provide all cyanobacteria and some chemoautotrophs with the ability to utilise limited environmental CO2 and function as a key component of CO2-concentrating mechanisms. In this chapter, we will summarise recent advances in understanding the composition, biogenesis, structural and functional regulation of carboxysomes, as well as synthetic engineering of carboxysomes.
Synthetic biology is here to stay and will transform agriculture if given the chance. The huge challenges facing food, fuel and chemical production make it vital to give synthetic biology that chance—notwithstanding the shifts in mindset, training and infrastructure investment this demands. Here, we assess opportunities for agricultural synthetic biology and ways to remove barriers to their realization. This Perspective assesses the opportunities and challenges for synthetic biology in revolutionizing agriculture, and highlights the resources and approaches we need to remove the barriers and propel another Green Revolution.
In this paper, we study adaptation mechanisms in a class of phosphorylation cycles where allosteric binding and gene autoregulation mechanisms regulate the phosphorylation processes. We show that both mechanisms enable a robust setpoint regulation of the regulator metabolite in the presence of constant, as well as, periodic external stimuli. The allosteric binding mechanism without the presence of gene autoregulation can serve as an integral controller. Furthermore, we show that the incorporation of a gene autoregulation mechanism enables the gene expression system to act as a genetic oscillator which allows for the adaptation mechanism to periodic external stimuli. These results provide a theoretical explanation to the cell homeostasis under quasi-constant environmental conditions, as well as, periodic biological rhythms.
Ensuring that one gene's transcription does not inappropriately affect the expression of its neighbors is a fundamental challenge to gene regulation in a genomic context. In plants, which lack homologs of animal insulator proteins, the mechanisms that prevent transcriptional interference are not well understood. Here we show that BORDER proteins are enriched in intergenic regions and prevent interference between closely spaced genes on the same strand by promoting the 3' pausing of RNA polymerase II at the upstream gene. In the absence of BORDER proteins, 3' pausing associated with the upstream gene is reduced and shifts into the promoter region of the downstream gene. This is consistent with a model in which BORDER proteins inhibit transcriptional interference by preventing RNA polymerase from intruding into the promoters of downstream genes.
Deep biosphere represents an unexplored realm of planetary life residing underneath the continental and oceanic crusts that constitutes majorly of prokaryotic life forms bacteria and archaea. Microbial communities which reside within various deep subsurface environments form a significant but largely unknown portion of the Earth’s biosphere. While the shallow aquifer and sedimentary rock microbiome might get access to the nutrient pool available above ground, deep subterranean habitats hosted by crystalline rocks are severely constrained by the availability of photosynthetically derived nutrients. Deep subsurface microbiome underneath the continental crusts not only showed variations based on their geographic locations but also with respect to the abundance of various microbial populations and their metabolic properties. It is estimated that the deep biosphere microorganisms represent the largest pool of carbon, nitrogen, and phosphorous and constitute a critical component of biogeochemical engine of our planet. The aphotic deep dark microbial realm that has evolved possibly billions of years ago has developed unique metabolic repertoire for their survival. The deep biosphere microbiome is considered to be a portion of planetary life with extraordinary life-supporting system that works beyond our notion about biological and physical constraints. Advancement of techniques in microbial ecology has enabled us to decipher deep subsurface microbiome which resides up to several kilometers below the surface using both cultivation-dependent and cultivation-independent techniques. In this chapter, we have summarized our understanding of the deep biosphere microbiome within terrestrial subsurface. Habitability of life within the deep subsurface has been discussed considering the major metabolic routes deployed by the microorganisms. Cultivation-dependent and cultivation-independent studies and their requirement and outcome from various exploratory researches have been documented. Techniques used for sampling the subsurface microbiome are discussed, highlighting the role of possible contamination during drilling and subsequent postcore extraction processes. Lastly, applications of deep subsurface microbiome research in achieving better sustainability and biotechnological innovations are discussed.
Glycation can be defined as an array of non-enzymatic post-translational modifications of proteins formed by their interaction with reducing carbohydrates and carbonyl products of their degradation. Initial steps of this process rely on reducing sugars and result in the formation of early glycation products—Amadori and Heyns compounds via Schiff base intermediates, whereas their oxidative degradation or reactions of proteins with α-dicarbonyl compounds yield a heterogeneous group of advanced glycation end products (AGEs). These compounds accompany thermal processing of protein-containing foods and are known to impact on ageing, pathogenesis of diabetes mellitus and Alzheimer’s disease in mammals. Surprisingly, despite high tissue carbohydrate contents, glycation of plant proteins was addressed only recently and its physiological role in plants is still not understood. Therefore, here we summarize and critically discuss the first steps done in the field of plant protein glycation during the last decade. We consider the main features of plant glycated proteome and discuss them in the context of characteristic metabolic background. Further, we address the possible role of protein glycation in plants and consider its probable contribution to protein degradation, methylglyoxal and sugar signalling, as well as interplay with antioxidant defense.
Phosphorylation dynamics of LHCSR3 were investigated in Chlamydomonas reinhardtii by quantitative proteomics and genetic engineering. LHCSR3 protein expression and phosphorylation were induced in high light. Our data revealed synergistic and dynamic N‐terminal LHCSR3 phosphorylation. Phosphorylated and non‐phosphorylated LHCSR3 associated with PSII‐LHCII supercomplexes. The phosphorylation status of LHCB4 was closely linked to the phosphorylation of multiple sites at the N‐terminus of LHCSR3, indicating that LHCSR3 phosphorylation may operate as a molecular switch modulating LHCB4 phosphorylation, which in turn is important for PSII‐LHCII disassembly. Notably, LHCSR3 phosphorylation diminished under prolonged high light, which coincided with onset of CEF. Hierarchical clustering of significantly altered proteins revealed similar expression profiles of LHCSR3, CRX and FNR. This indicates the existence of a functional link between LHCSR3 protein abundance and phosphorylation, photosynthetic electron flow and the oxidative stress response.
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How can the evolutionary success of prokaryotes be explained? How did they manage to survive conditions that have fluctuated, with drastic events over 3.5 billion years? Which significant metabolisms and mechanisms have appeared over the course of evolution that have permitted them to survive the most inhospitable conditions from the physicochemical point of view? In a “Red Queen Race,” prokaryotes have always run sufficiently fast to adapt to constraints imposed by the environment and the other living species with which they have established interactions. If the criterion retained to define the level of evolution of an organism is its capacity to survive and to yield the largest number of offsprings, prokaryotes must be considered highly evolved organisms.
Significance
To optimize photosynthetic performance and minimize photooxidative damage, photosynthetic organisms evolved to efficiently balance light energy absorption and electron transport with cellular energy requirements under constantly changing light conditions. The regulation of linear electron flow (LEF) and cyclic electron flow (CEF) contributes to this fine-tuning. Here we present a model of the formation and structural molecular organization of a CEF-performing photosystem I (PSI)–light harvesting complex I (LHCI)–cytochrome (cyt) b 6 f supercomplex from the green alga Chlamydomonas reinhardtii . Such a structural arrangement could modulate the distinct operation of LEF and CEF to optimize light energy utilization, despite the same individual structural units contributing to these two different functional modes.
Pathways replenishing tricarboxylic acid cycle were divided into four major groups based on metabolite serving as source for oxaloacetic acid or other tricarboxylic acid cycle component synthesis. Using this metabolic map, the analysis of genetic potential for functioning of tricarboxylic acid cycle replenishment pathways was carried out for seven strains of purple non-sulfur bacterium Rhodopseudomonas palustris. The results varied from strain to strain. Published microarray data for phototrophic acetate cultures of Rps. palustris CGA009 were analyzed to validate activity of the putative pathways. All the results were compared with the results for another purple non-sulfur bacterium, Rhodobacter capsulatus SB1003 and species-specific differences were clarified.
Methane and methanol are regarded as alternative and highly attractive nonfood raw materials for the biotechnology sector. The supply of methane and methanol comes from both fossil and renewable resources, rendering them flexible and sustainable raw materials. Reduced one-carbon (C1) compounds are used by specialized groups of microorganisms, i.e., the methylotrophs, as their sole source of carbon and energy. While progress to engineer and use natural methylotrophs in biotechnology is ongoing, synthetic methylotrophs only recently have gained interest as a parallel approach both in academia and private industry. Synthetic methylotrophy refers to the design and rational engineering of methylotrophy to established non-methylotrophic production hosts for access to methane and methanol as feedstock while maintaining their biotechnological production potential. In this chapter, we will illustrate how combined systems and synthetic biology approaches capitalize on the metabolic versatility and engineered production pathways of industrially well-established microorganisms, such as Escherichia coli, Bacillus subtilis, and Corynebacterium glutamicum, for biotransformation from methane and methanol. Challenges and current prospects for designing and engineering the next generation of synthetic methylotrophs are also discussed.
1. Chlorella pyrenoidosa wurde in phosphatfreiem Medium suspendiert und nach entsprechender Vorbehandlung in 6-proz. Trichloressigsäure (TES) abgetötet und extrahiert. Das im TES-Auszug bestimmbare anorganische Phosphat wies in den ersten 30 Sek. nach Beginn der Belichtung eine Verminderung um 20%, in den ersten 90 Sek. nach der Verdunklung eine Vermehrung um 30% auf, während die stationären Licht- und Dunkelzustände keine wesentlichen Verschiebungen hervorriefen.
2. Eine kurzdauernde Atmungssteigerung im Anschluß an eine Belichtungsperiode konnte beobachtet und mit den Phosphatspiegelschwankungen in Zusammenhang gebracht werden.
3. In diesen Beobachtungen wird der Beweis für die seit einiger Zeit diskutierte Ansicht, daß ein Teil der Lichtenergie auf dem Wege über das energiereiche Phosphat in „chemische Energie“ umgewandelt wird, gesehen.
4. Die Möglichkeiten der Phosphatbindung im Rahmen der photochemischen Reaktionskette werden besprochen und in entsprechende Schemata eingebaut.
5. Als primäre Produkte der Photoreaktion werden ein an einen H-Acceptor mittleren Potentials gebundener Wasserstoff und energiereiche Phosphate angesehen. Mit deren Hilfe könnte nicht nur die CO2-Assimilation, sondern auch die Reduktion und der Einbau von Nitrat und Sulfat und der Umbau von Kohlenhydraten und anderer sauerstoffreicher Verbindungen zu sekundären Pflanzenstoffen und Wuchsstoffen durchgeführt werden. Ein entsprechendes Schema der Photosynthese wird entworfen.
Versuche über Zerfall und Wiederaufbau der Glutaminsäure in lebender Chlorella und über den Zusammenhang zwischen Glutaminsäure und Photosynthese.
Bei verarmten Suspensionen von Chlorella pyrenoidosa wurde der Glucoseeinbau im Dunkeln und im Licht in Abhängigkeit von verschiedenen Außenbedingungen untersucht. Dabei ergab sich, daß in einem p
Die gesteigerte Glucoseaufnahme im Licht tritt bei frisch geernteten oder mit Glucose vorgefütterten Algen nicht auf. Wird dagegen gleichzeitig mit Glucose und Nitrat vorgefüttert, so bleibt der Effekt, wenn auch vermindert, erhalten.
Unter anaeroben Bedingungen wird im saueren p
Es wird angenommen, daß bei verarmten Algen der Glucoseeinbau durch den Vorrat an ATP begrenzt ist und durch zusätzliche ATP-Lieferung im Zusammenhang mit der Photosynthese bis zur Sättigung der Hexokinase bzw. der Phosphorylase gesteigert werden kann. Bei längerer Belichtung bzw. Vorfütterung stauen sich Assimilationsprodukte auf und vermindern die Durchsatzgeschwindigkeit des Fermentsystems, so daß die ATP nicht mehr Minimumfaktor und damit für die Reaktionsgeschwindigkeit unwichtig ist. Bei verarmten Chlorellen kann daher der gesteigerte Glucoseeinbau im Licht als Indikator einer lichtabhängigen Phosphorylierung aufgefaßt werden.
• Short-term photosynthetic experiments using C¹⁴O2 and paper chromatography were performed with 27 different plants representing nine phyla: Schizophyta (Schizophyceae), Euglenophyta, Chlorophyta, Charophyta, Chrysophyta, Rhodophyta, Bryophyta, Pteridophyta, and Spermatophyts.
• There is a remarkable uniformity in the types of ethanol-soluble compounds which became radioactive in the entire group of plants used. The amounts of the different compounds varied considerably percentagewise among the various plants as would be expected because of their inherent metabolic differences and the variations in their physiological states induced by experimental conditions.
• Sucrose became radioactive in very different amounts in two major groupings of plants: (a) those containing only photosynthetic tissue, and (b) those containing non-photosynthetic tissue as well. The amount of radioactive sucrose in the former group was much lower than that in the latter.
• An unidentified compound became radioactive in appreciable amounts in two of the blue-green algae, but was radioactive in very small amounts or not visible at all on the chromatograms of all other plants.
The metabolism of C{sup 14} labeled glycolic acid by Scenedesmus has been studied using radiochromatographic techniques for the separation and identification of products. When the pH of the medium was 2.8, appreciable assimilation occurred. The products were identical to those observed in C{sup 14}O{sub 2} photosynthesis. A major reaction anaerobically in the dark resulted in incorporation of C{sup 14} in almost equal amounts in the glycine and serine reservoirs. When the algae were illuminated, a diminution in the amount of glycine was observed.
1. The isolated chloroplasts from Stellaria media show a progressive fall in activity approaching zero in 3-6 hr. Four different strains of the plant were grown which showed differences in the stability of chloroplasts after removal. 2. Two methods have been used to measure the activity of chloroplasts: (a) The measurement with HbO2 of oxygen produced from ferric potassium oxalate as previously described. (b) The measurement of the rate of reduction of methaemoglobin in presence of atmospheric oxygen, the methaemoglobin being reduced by the ferrous iron. 3. The QO_2, measured as rate of oxygen production calculated on the basis of dry weight of leaf taken, is about 20. The QO_2, measured as rate of methaemoglobin reduction, generally appeared less as the reduction of methaemoglobin by ferrous iron is relatively slow. 4. The reduction of methaemoglobin in presence of ferric potassium oxalate has been studied quantitatively from the point of view of iron, methaemoglobin, and chloroplast concentration. 5. The effect of different light intensities on the ferric oxalate reaction is similar to the effect of varying light intensity on photosynthesis in whole plants and lies within the range of values found by different workers. 6. The ferric oxalate reaction is inhibited by urethane. Phenyl urethane inhibits in much smaller concentrations than ethyl urethane. The effective concentrations of urethane are similar to those affecting photosynthesis. 7. It is concluded from the present observations that the light reaction in vegetable photosynthesis is the production of the oxygen molecule and is not the reduction of carbon dioxide.
THE high affinity for oxygen possessed by muscle hæmoglobin suggested its use as a very sensitive spectroscopic method for detecting and measuring small quantities of oxygen1. This method has now been applied to study the oxygen evolution of isolated chloroplasts exposed to light. While being much less sensitive than the bacterial methods which have been successfully applied in the past, the hæmoglobin method (originally used by Hoppe-Seyler to demonstrate oxygen from green plants) has the advantage of giving the measure of oxygen. A solution of hæmoglobin containing 0.45 × 10-4 gm. atoms of iron per litre, is equivalent to 1 c.mm. of oxygen per c.c.; the degree of saturation can be determined spectroscopically with an accuracy of 5 per cent.
Photosynthesizing plants have been exposed to C 14O 2 for short periods of time (0.4 to 15 sec.) and the products of carbon dioxide reduction analyzed by paper chromatography and radioautography. Methods have been developed for the degradation of ribulose and sedoheptulose. These sugars, obtained as their phosphate esters from the above C 14O 2 exposures and from other experiments, have been degraded and their distribution of radiocarbon determined. The distribution of radiocarbon in these sugars, and other data, indicate that sedoheptulose phosphate and ribulose diphosphates are formed during photosynthesis from triose and hexose phosphates, the latter being synthesized, in turn, by the reduction of 3-phosphoglyceric acid. Further evidence has been found for the previously proposed carboxylation of ribulose diphosphate to phosphoglyceric acid. Free energy calculations indicate this step would proceed spontaneously if enzymatically catalyzed. The efficiency of this cycle for reduction of CO 2 to hexose would be 0.9 if the reduction of each molecule of PGA requires the concurrent conversion of one molecule of ATP and one of DPN (red) to ADP, inorganic phosphate and DPN (ox.).
Techniques have been developed and an apparatus has been designed and constructed to make possible quantitative experiments in photosynthesis. It is now possible to measure the amounts of the photosynthetic intermediates as a function of external variables such as partial pressure of CO2 and O2, light, temperature, pH, poisons, and various combinations of these. Use has been made of the above techniques to study the transient changes taking place when the carbon dioxide pressure is varied and these results have led to the development of the concept of fluctuating reservoir sizes. These data also have provided the first unequivocal evidence of the relation of phosphoglyceric acid and ribulose diphosphate to the carbon dioxide incorporation step. Ribulose diphosphate has been identified as being closely related to, if not actually, the carbon dioxide acceptor and phosphoglyceric acid as being the product of the carboxylation. The data show that ribulose monophosphate and triose phosphate are also in the cycle which regenerates the carbon dioxide acceptor, and provide us with the precursor-product relationships between the compounds in this cycle. The kinetics of free glycolic acid provide strong evidence of the presence of a transketolase enzyme system which transfers an unphosphorylated glycolyl fragment. Perhaps the most important result of this work is the insight it gives into the complicated, finely balanced system of interrelated chemical reactions we call life.
Studies of the transient changes in radiocarbon found in various photosynthetic and respiratory intermediates in Scenedesmus which result when changing from a condition of steady state photosynthesis in the light to dark and then back to light again indicate the following metabolic mechanisms: (1) The carboxylation step in the carbon reduction cycle of photosynthesis results in the formation of two molecules of 3-PGA from one RuDP molecule, one CO 2 and one H 2O. (2) This carboxylation reaction proceeds for about 30 seconds in the dark after turning off the light, its rate being proportional to the falling concentration of RuDP, and stops when the latter concentration falls to zero. (3) Turning off the light results in the transfer of radiocarbon from PGA to citric acid, and glutamic acid. Turning on the light results in a decrease in radiocarbon in citric acid. These results provide new evidence for the theory that the oxidation of pyruvic acid to acetyl CoA and CO 2 with a subsequent condensation of acetyl CoA with oxaloacetic acid to give citric acid is blocked in the light by reduction of a cofactor, which may be thioctic acid, required for pyruvic acid oxidation. (4) These transients in radioactivity found in Krebs cycle acids are taken as evidence for the association with the chloroplast of enzymes and intermediates of the Krebs cycle.
Green algae have been treated with ranioactive KCN in an investigation of the action of cyanide on photosynthesis. A multitude of products have been found to be formed in very short exposures (10--15 sec). One of these products has been identified with the product formed when the algae are given radioactive CO/sub 2/ and non-radioactive KCH. The same product has been synthesized by a non-enzymatic cyanohydrin addition roaction on ribulose 1,5-diphosphate. It has been shown to be a 2-carboxy-pentitol (probably mostly ribitol) 1,5diphosphate. Upon hydrolysis it gives an hydroxy acid (or mixture of isomers) closely related to hamamelonic acid. The significance of this and the other as yet unidentified products of cyanide interaction with a biological system is discussed with respect to the use of cyanide as an inhibitor. (auth)
1. Paper chromatography has been employed to separate the radioactive products formed during photosynthesis in C14O2. 2. The method has been used for the separation and identification of carboxylic acids and phosphate esters. 3. The first observed product of carbon dioxide assimilation during photosynthesis has been isolated and shown to be phosphoglyceric acid.
Die Trennung des Phänomens der Photosynthese grüner Pflanzen in eine Lichtreaktion und die vom Licht unabhängige Reduktion der Kohlensäure werden diskutiert.
Die Reduktion der Kohlensäure und das Schicksal des assimilierten Kohlenstoffs wurden untersucht mit Hilfe der Spurenmethode (Markierung der assimilierten Kohlensäure mit C14) und der Papierchromatographie. Ein Reaktionszyklus wird vorgeschlagen, in dem Phosphoglyzerinsäure das erste isolierbare Assimilationsprodukt ist.
Analysierung des Extraktes von Algen, die in einem stationären Zustand für längere Zeit radioaktive Kohlensäure assimilierten, lieferte weitere Auskunft über den vorgeschlagenen Zyklus und gestattete, die am Zyklus beteiligten Mengen einiger Substanzen ungefähr zu bestimmen. Die frühere Vermutung, dass Licht den Respirationszyklus beeinflusst, wird bestätigt. Die Möglichkeit der Mitwirkung von α-Liponsäure (α-lipoic acid) oder einer verwandten Substanz, bei diesem Effekt und im Photosynthesezyklus, wird erörtert.
Thesis (Ph. D. in Chemistry)--University of California, Berkeley, Sept. 1960. Includes bibliographical references (leaves 186-201).
Aus: Zeitschrift f. Botanik. Bd 32, H. 4. Berlin, Math.-naturwiss. Diss., 1937 (Nicht f. d. Austausch).
Contenido : I. Cromatografía en papel: introducción; teoría de la c. en p.; métodos generales; métodos cuantitativos; aminoácidos, aminas y proteínas; carbohidratos; ácidos alifáticos; ácidos esteroides y bile; purinas, pirimidinas y sustancias relacionadas; fenoles, ácidos aromáticos y porfirinas; sustancias orgánicas misceláneas; antibióticos y vitaminas; separaciones inorgánicas. II. Electroforesis en papel: Introducción; teoría general; métodos; dos técnicas dimensionales; electroforesis continua; algunas consideraciones cuantitativas.
SUMMARY Citrulline has been isolated and identified from extracts of Nostoc muscorum. All members of the Cyanophyceae hitherto investigated show a relatively large amount of the CO2 fixed during photosynthesis in citrulline (ranging as high as 20 per cent. in Nostoc) when compared to the trace amounts found in the Chlorophyceae. Nostoc also has the ability to fix C14 in citrulline during dark fixation, but at a rate slower than in light.
As no free urea or arginine was found in Nostoc, it is likely that citrulline is functioning in reactions other than those leading to arginine and urea synthesis.
Other possible functions for citrulline are briefly discussed.
Uptake of CO2 in photosynthesis was stopped by adding high concentrations of cyanide to Chlorella suspensions after short-time exposure to C14O2. If illumination is continued for several seconds before the algae are extracted with alcohol, there is a strong change in the distribution of radioactivity between the different substances analyzed by paper chromatography. The relative activity of PGA drops to about 10%, whereas other monophosphates and especially diphosphates rise strongly. After dephosphorylation of the diphosphate area two new radioactive spots were noticed. Preliminary experiments have shown that it is probably the acid and lactone form of a polyhydroxy acid.
1.1. The total C14O2 fixation by algae has been determined for three different modes of killing the algae. The method of C14 measurement involved the direct plating from an acid medium of the algae suspension, or some fractions thereof, and counting by thin-walled, end-window Geiger counters.2.2. When the algae are killed by dropping into acetone at subzero temperatures, a higher count appears on the plate than when they are killed by dropping them into boiling ethanol.3.3. The percentage difference is greater the shorter the photosynthesis time.4.4. The addition of hydroxylamine to the algae just prior to killing with acetone increases the apparent total plate count as well as that of the acetone-soluble fraction.
1.1. Using the acid-tolerant alga, Chlorella Marburg St., it was observed that the sodium fluoride-induced carbon dioxide burst was present. However, a 1:1 ratio between chlorophyll and carbon dioxide evolved during this burst was seldom realized. Yields upward of 400% (on a chlorophyll basis) were obtained.2.2. It was found that the size of the carbon dioxide burst was not stable and decreased if longer periods of anaerobisity were maintained, and that it increased if the thick algal suspensions were allowed to respire. The source of the carbon dioxide seems to be closer to the intermediary metabolism of respiration and fermentation than to photosynthesis.3.3. The source of the carbon dioxide gush could not be removed by preillumination of algal suspensions under a nitrogen atmosphere. Such treatment, on the contrary, helped to stabilize the size of the burst, as did the addition of glucose in the dark. Such results are incompatible with the idea of a chlorophyll-carbon dioxide complex as the substrate for the photochemical process.4.4. The effect of sodium fluoride on photosynthesis of green algae was found to be complex. In some instances complete inhibition occurred, whereas in other experiments no inhibition occurred although a carbon dioxide gush was evident.