不同二氧化碳浓度培养对两株栅藻碳固定速率及油脂积累的影响

正人类在利用化石燃料的过程中会导致大量有害温室气体CO_2的排放,促进全球气候变暖。微藻可通过光合作用固定CO_2,同时大量的微藻生物质还能作为生物能源的原料[1],因此,越来越多的研究关注于微藻生物固碳以达到降低碳排放的目的。利用微藻光合作用进行CO_2固定是一种能量节约型和环境友好型技术手段[2]。在利用微藻进行CO_2生物固定以及生物燃料生产时,研究微藻的CO_2固定能力、CO_2对微藻的生长以及油脂积累的影响等都是十分重要的。国内外利用微藻进行生     

微生物电合成-电能驱动的CO_2固定

CO_2代表着地球上最广泛的可再生资源,通过生物固碳途径将CO_2转化为有机物,是生产生物燃料和生物基化学品的重要方向,由于能量供给不足和微生物自身生理代谢的限制,生物固碳效率还有待提高.利用电能驱动微生物还原CO_2是实现CO_2高效转化的新策略,被称为微生物电合成.本文从电合成微生物种类、胞外电子传递、电极材料等方面综述了微生物电合成的研究进展,并对微生物电合成的未来研究方向进行了展望.     

CO_2固定的合成生物学

将CO2转化为燃料或化学品,实现CO2的资源化利用,是缓解化石能源枯竭和温室效应这两大问题的有效途径之一.自养生物能够以光能/氢气/硫等为能量来源,在常温常压下将CO2转化为有机物,提供了一种CO2资源化利用的途径.利用经过代谢工程改造的自养生物(如蓝藻),已经可以实现从CO2生物合成十余种化学品,但整体固碳和转化效率尚低,不能满足工业应用的需求.本文首先介绍了目前已发现的6条天然生物固碳途径,重点从固碳途径及能量供给两方面总结了近年来生物固碳合成生物学研究取得的进展,并对生物固碳的前景和未来方向进行了展望.     

农田土壤固碳措施的温室气体泄漏和净减排潜力

农田土壤固碳措施作为京都议定书认可的大气CO2减排途径受到了广泛关注.研究表明,农田土壤固碳措施在主要农业国家和全球都具有很大的固碳潜力.但是,实施农田土壤固碳措施有可能影响农业中化石燃料消耗和其他农业投入的CO2排放和非CO2温室气体排放.这些土壤碳库以外的温室气体排放变化可能抵消部分甚至全部土壤固碳效果,构成了农田土壤固碳措施的温室气体泄漏.因此,将土壤固碳和温室气体泄漏综合计算的净减排潜力成为了判定土壤固碳措施可行性的首要标准.综述总结了目前较受重视的一些农田措施(包括施用化学氮肥、免耕和保护性耕作、灌溉、秸秆还田、施用禽畜粪便以及污灌)的土壤固碳潜力,温室气体泄漏和净减排潜力研究成果.结果表明,温室气体泄漏可抵消以上措施土壤固碳效益的-241%～660%.建议在今后的研究中,应该关注土壤碳饱和、气候变化及土地利用变化对农田固碳措施温室气体泄漏和净减排潜力的评估结果的影响.     

一碳气体利用微生物及其基因工程改造

一碳气体主要包括CO、CO_(2)和CH_(4)等,这些气体来源于陆地生物活动、工业废气以及气化合成气等,其中CO_(2)与CH_(4)是温室气体,对全球气候变化有着重要的影响。利用微生物进行一碳气体生物转化既可以解决废气排放的问题,又能生产燃料及多种化学品。近年来,运用CRISPR/Cas9等基因编辑技术对一碳气体利用微生物进行改造,是提高它们的产物得率、增加产物类型的重要途径。本文主要围绕甲烷营养菌、自养乙酸菌、一氧化碳营养菌等一碳气体利用微生物,综述了其生物学特性、好氧和厌氧代谢途径、代谢产物,以及常用的基因编辑技术(利用同源重组的基因中断技术、二类内含子ClosTron法、CRISPR/Cas基因编辑及以噬菌体重组酶介导的DNA大片段引入等)在它们中的应用,为后续相关研究提供参考。     

碳一气体生物利用进展

近年来,随着经济的快速发展和人们对于资源需求的增长,化石燃料的使用越来越多,这一方面加剧了能源的过度消耗,另一方面导致了环境污染和温室效应加重。为了在保护环境的同时有效地利用资源,越来越多的研究集中在通过细胞工厂平台进行能源和化学品的生物合成。利用特定的微生物(如嗜甲烷菌、微藻和梭菌等)可以将温室气体和合成气中的碳一成分通过发酵过程转化为能源和化学品。本文中,笔者详细讨论了不同微生物转化3种碳一气体(CH_4、CO_2和CO)的生物代谢途径、关键合成酶、最终代谢产物和生物转化过程的优化及放大。     

食气梭菌的研究进展

食气梭菌是一类主要的化能自养微生物,可利用二氧化碳(CO_2)和一氧化碳(CO)合成多种化学品和燃料,具有良好的工业应用前景。天然的食气梭菌吸收、固定和转化一碳气体速率较慢,能量代谢效率低且高值产物种类少。近年来,随着组学、分子遗传学工具以及生化分析技术的快速发展,食气梭菌的生理代谢特点及其相关分子机制、代谢工程设计、改造和发酵工艺等方面都得到广泛而深入的研究。本文针对近年来食气梭菌的研究进展进行了梳理和总结,以期能为这类重要工业微生物的基础和应用研究,以及一碳气体的生物转化利用提供参考。     

微生物固碳的电子供给策略研究进展北大核心CSCD

随着生物化工技术的不断发展成熟,通过改造微生物已可以实现二氧化碳、甲烷等温室气体的固定、转化和利用,而电子传递及能量供给对微生物固碳效率起着决定性的作用。本文首先分析了好氧性嗜甲烷菌、化能自养微生物等天然微生物细胞内外的直接、间接电子传递系统。在此基础上,围绕微生物固碳细胞工厂的构建,进一步介绍了基于光能、电能的人工电子供给策略及其对固碳过程中代谢通量、合成路径和供能效率的影响。最后针对微生物固碳的关键共性技术难点,简要展望了可行性的解决方案及相关应用前景。     

甲烷生物利用及嗜甲烷菌的工程改造

作为来源广泛、储量丰富的有机碳一气体,甲烷被认为是下一代工业生物技术中最具潜力的碳原料之一。嗜甲烷菌能够利用其体内的甲烷单加氧化酶,将甲烷作为唯一的碳源和能源进行生长和代谢,这为温室气体减排及其开发利用提供了新的策略。目前,嗜甲烷菌生物催化体系的相关研究已开展多年,随着系统生物学和合成生物学的快速发展,利用代谢工程合理改造嗜甲烷菌代谢途径以提高甲烷转化效率,已经实现了生物转化甲烷制备多种大宗化学品和生物燃料。本文详细讨论并介绍了嗜甲烷菌催化氧化甲烷的相关代谢途径、高效细胞工厂构建及部分化学品生物合成的最新研究进展,并对甲烷生物转化未来的发展方向和面临的技术挑战进行了讨论和展望。     

琥珀酸生物合成过程中CO_2代谢调控的研究进展

作为重要的四碳平台化合物,琥珀酸被美国能源部列为12种最具潜力的大宗生物基化学品之首.CO_2作为琥珀酸合成的必需底物,是决定琥珀酸合成效率的关键因素.本文从CO_2溶解、转运及转化、固定和组合调控4个方面系统评述了琥珀酸生物合成过程中CO_2代谢调控的研究进展,并探讨了CO_2调控策略的未来发展方向.     

Computation of metabolic fluxes and efficiencies for biological carbon dioxide fixation

With rising energy prices and concern over the environmental impact of fossil fuel consumption, the push to develop biomass derived fuels has increased significantly. Although most global carbon fixation occurs via the Calvin Benson Bassham cycle, there are currently five other known pathways for carbon fixation; the goal of this study was to determine the thermodynamic efficiencies of all six carbon fixation pathways for the production of biomass using flux balance analysis. The three chemotrophic pathways, the reductive acetyl-CoA pathway, the 3-hydroxypropionate/4-hydroxybutyrate cycle and the dicarboxylate/4-hydroxybutyrate cycle, were found to be more efficient than photoautotrophic carbon fixation pathways. However, as hydrogen is not freely available, the energetic cost of hydrogen production from sunlight was calculated and included in the overall energy demand, which results in a 5 fold increase in the energy demand of chemoautotrophic carbon fixation. Therefore, when the cost of hydrogen production is included, photoautotrophic pathways are more efficient. However, the energetic cost for the production of 12 metabolic precursors was found to vary widely across the different carbon fixation pathways; therefore, different pathways may be more efficient at producing products from a single precursor than others. The results of this study have significant impact on the selection or design of autotrophic organisms for biofuel or biochemical production. Overall biomass production from solar energy is most efficient in organisms using the reductive TCA cycle, however, products derived from one metabolic precursor may be more efficiently produced using other carbon fixation pathways.     

Genomic analysis of carbon monoxide utilization and butanol production by Clostridium carboxidivorans strain P7

Increasing demand for the production of renewable fuels has recently generated a particular interest in microbial production of butanol. Anaerobic bacteria, such as Clostridium spp., can naturally convert carbohydrates into a variety of primary products, including alcohols like butanol. The genetics of microorganisms like Clostridium acetobutylicum have been well studied and their solvent-producing metabolic pathways characterized. In contrast, less is known about the genetics of Clostridium spp. capable of converting syngas or its individual components into solvents. In this study, the type of strain of a new solventogenic Clostridium species, C. carboxidivorans, was genetically characterized by genome sequencing. C. carboxidivorans strain P7(T) possessed a complete Wood-Ljungdahl pathway gene cluster, involving CO and CO(2) fixation and conversion to acetyl-CoA. Moreover, with the exception of an acetone production pathway, all the genetic determinants of canonical ABE metabolic pathways for acetate, butyrate, ethanol and butanol production were present in the P7(T) chromosome. The functionality of these pathways was also confirmed by growth of P7(T) on CO and production of CO(2) as well as volatile fatty acids (acetate and butyrate) and solvents (ethanol and butanol). P7(T) was also found to harbour a 19 Kbp plasmid, which did not include essential or butanol production related genes. This study has generated in depth knowledge of the P7(T) genome, which will be helpful in developing metabolic engineering strategies to improve C. carboxidivorans's natural capacity to produce potential biofuels from syngas.     

Regulators of nonsulfur purple phototrophic bacteria and the interactive control of CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy generation

For the metabolically diverse nonsulfur purple phototrophic bacteria, maintaining redox homeostasis requires balancing the activities of energy supplying and energy-utilizing pathways, often in the face of drastic changes in environmental conditions. These organisms, members of the class Alphaproteobacteria, primarily use CO2 as an electron sink to achieve redox homeostasis. After noting the consequences of inactivating the capacity for CO2 reduction through the Calvin-Benson-Bassham (CBB) pathway, it was shown that the molecular control of many additional important biological processes catalyzed by nonsulfur purple bacteria is linked to expression of the CBB genes. Several regulator proteins are involved, with the two component Reg/Prr regulatory system playing a major role in maintaining redox poise in these organisms. Reg/Prr was shown to be a global regulator involved in the coordinate control of a number of metabolic processes including CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy-generation pathways. Accumulating evidence suggests that the Reg/Prr system senses the oxidation/reduction state of the cell by monitoring a signal associated with electron transport. The response regulator RegA/PrrA activates or represses gene expression through direct interaction with target gene promoters where it often works in concert with other regulators that can be either global or specific. For the key CO2 reduction pathway, which clearly triggers whether other redox balancing mechanisms are employed, the ability to activate or inactivate the specific regulator CbbR is of paramount importance. From these studies, it is apparent that a detailed understanding of how diverse regulatory elements integrate and control metabolism will eventually be achieved.     

Improving photosynthesis and metabolic networks for the competitive production of phototroph-derived biofuels

To improve bioenergy production from photosynthetic microorganisms it is necessary to optimize an extensive network of highly integrated biological processes. Systematic advances in pathway engineering and culture modification have resulted in strains with increased yields of biohydrogen, lipids, and carbohydrates, three bioenergy foci. However, additional improvements in photosynthetic efficiency are necessary to establish a viable system for biofuel production. Advances in optimizing light capture, energy transfer, and carbon fixation are essential, as the efficiencies of these processes are the principal determinants of productivity. However, owing to their regulatory, catalytic, and structural complexities, manipulating these pathways poses considerable challenges. This review covers novel developments in the optimization of photosynthesis, carbon fixation, and metabolic pathways for the synthesis of targeted bioenergy carriers.     

Compartmentation in plant metabolism

Cell fractionation and immunohistochemical studies in the last 40 years have revealed the extensive compartmentation of plant metabolism. In recent years, new protein mass spectrometry and fluorescent-protein tagging technologies have accelerated the flow of information, especially for Arabidopsis thaliana, but the intracellular locations of the majority of proteins in the plant proteome are still not known. Prediction programs that search for targeting information within protein sequences can be applied to whole proteomes, but predictions from different programs often do not agree with each other or, indeed, with experimentally determined results. The compartmentation of most pathways of primary metabolism is generally covered in plant physiology textbooks, so the focus here is mainly on newly discovered metabolic pathways in plants or pathways that have recently been revised. Ultimately, all of the pathways of plant metabolism are interconnected, and a major challenge facing plant biochemists is to understand the regulation and control of metabolic networks. One of the best-characterized networks links sucrose synthesis in the cytosol with photosynthetic CO(2) fixation and starch synthesis in the chloroplasts. One of the key features of this network is how the transport of pathway intermediates and signal metabolites across the chloroplast envelope conveys information between the two compartments, influencing the regulation of several enzymes to co-ordinate fluxes through the different pathways. It is widely accepted that chloroplasts and mitochondria originated from prokaryotic endosymbionts, and that new transporters and regulatory networks evolved to integrate metabolism in these organelles with the rest of the cell. Curiously, the present-day locations of many metabolic pathways within the cell often do not reflect their evolutionary origin, and there is evidence of extensive shuffling of enzymes and whole pathways between compartments during the evolution of plants.     

Light-energy conversion in engineered microorganisms

Increasing interest in renewable resources by the energy and chemical industries has spurred new technologies both to capture solar energy and to develop biologically derived chemical feedstocks and fuels. Advances in molecular biology and metabolic engineering have provided new insights and techniques for increasing biomass and biohydrogen production, and recent efforts in synthetic biology have demonstrated that complex regulatory and metabolic networks can be designed and engineered in microorganisms. Here, we explore how light-driven processes may be incorporated into nonphotosynthetic microbes to boost metabolic capacity for the production of industrial and fine chemicals. Progress towards the introduction of light-driven proton pumping or anoxygenic photosynthesis into Escherichia coli to increase the efficiency of metabolically-engineered biosynthetic pathways is highlighted.     

Proteome and membrane fatty acid analyses on Oligotropha carboxidovorans OM5 grown under chemolithoautotrophic and heterotrophic conditions

Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium able to utilize CO and H(2) to derive energy for fixation of CO(2). Thus, it is capable of growth using syngas, which is a mixture of varying amounts of CO and H(2) generated by organic waste gasification. O. carboxidovorans is capable also of heterotrophic growth in standard bacteriologic media. Here we characterize how the O. carboxidovorans proteome adapts to different lifestyles of chemolithoautotrophy and heterotrophy. Fatty acid methyl ester (FAME) analysis of O. carboxidovorans grown with acetate or with syngas showed that the bacterium changes membrane fatty acid composition. Quantitative shotgun proteomic analysis of O. carboxidovorans grown in the presence of acetate and syngas showed production of proteins encoded on the megaplasmid for assimilating CO and H(2) as well as proteins encoded on the chromosome that might have contributed to fatty acid and acetate metabolism. We found that adaptation to chemolithoautotrophic growth involved adaptations in cell envelope, oxidative homeostasis, and metabolic pathways such as glyoxylate shunt and amino acid/cofactor biosynthetic enzymes.     

Review article. A re-evaluation of the ATP:NADPH budget during C3 photosynthesis: a contribution from nitrate assimilation and its associated respiratory activity?

The purpose of this review in reanalysing the ATP:reductant balance in illuminated leaf cells is to stress that the photosynthesis in vivo does not involve CO2 fixation alone, but embraces other processes, chief among which is N assimilation. Prior to the demonstration of CO2 fixation and photophosphorylation by isolated chloroplasts, the mitochondria were thought likely to provide all the ATP required for CO2 fixation (discussed in Arnon et al., 1954). During the 1960s, the development of techniques for the isolation of chloroplasts able to fix CO2 at rates approaching those of the parent tissue induced a paradigm shift, leading to the establishment of a dominant (if not unanimous) view that chloroplasts in vivo must by themselves meet all their ATP requirements. More recent studies, however, indicate that the reality lies somewhere between these two extremes. The present work places emphasis on the integrated nature of photosynthesis and proposes that much of the respiratory ATP necessary for whole cell photosynthesis may be generated during the production of C skeletons for N assimilation. Rather than considering dissipative electron transport pathways as necessary to uncouple respiratory precursor synthesis from ATP production, the present analysis emphasizes the metabolic value of ATP produced during N-linked respiration, with cellular ATP supply being tailored to ATP demand.     

Geochemical constraints on chemolithoautotrophic reactions in hydrothermal systems

Thermodynamic calculations provide the means to quantify the chemical disequilibrium inherent in the mixing of redeuced hydrothermal fluids with seawater. The chemical energy available for metabolic processes in these environments can be evaluated by taking into account the pressure and temperature dependence of the apparent standard Gibbs free energies of reactions in the S-H₂-H₂O system together with geochemical constraints on pH, activities of aqueous sulfur species and fugacities of H₂ and/or O₂. Using present-day mixing of hydrothermal fluids and seawater as a starting point, it is shown that each mole of H₂S entering seawater from hydrothermal fluids represents about 200,000 calories of chemical energy for metabolic systems able to catalyze H₂S oxidation. Extrapolating to the early Earth, which was likely to have had an atmosphere more reduced than at present, shows that this chemical energy may have been a factor of two or so less. Nevertheless, mixing of hydrothermal fluids with seawater would have been an abundant source of chemical energy, and an inevitable consequence of the presence of an ocean on an initially hot Earth. The amount of energy available was more than enough for organic synthesis from CO₂ or CO, and/or polymer formation, indicating that the vicinity of hydrothermal systems at the sea floor was an ideal location for the emergence of the first chemolithoautotrophic metabolic systems.