Biochemistry: Tackling unintelligent design

Room-temperature serial synchrotron crystallography structure of Spinacia oleracea RuBisCO

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the enzyme responsible for the first step of carbon dioxide (CO2) fixation in plants, which proceeds via the carboxylation of ribulose 1,5-biphosphate. Because of the enormous importance of this reaction in agriculture and the environment, there is considerable interest in the mechanism of fixation of CO2 by RuBisCO. Here, a serial synchrotron crystallography structure of spinach RuBisCO is reported at 2.3 Å resolution. This structure is consistent with earlier single-crystal X-ray structures of this enzyme and the results are a good starting point for a further push towards time-resolved serial synchrotron crystallography in order to better understand the mechanism of the reaction.

Improving Crop Yield through Increasing Carbon Gain and Reducing Carbon Loss

Photosynthesis is a process where solar energy is utilized to convert atmospheric CO2 into carbohydrates, which forms the basis for plant productivity. The increasing demand for food has created a global urge to enhance yield. Earlier, the plant breeding program was targeting the yield and yield-associated traits to enhance the crop yield. However, the yield cannot be further improved without improving the leaf photosynthetic rate. Hence, in this review, various strategies to enhance leaf photosynthesis were presented. The most promising strategies were the optimization of Rubisco carboxylation efficiency, the introduction of a CO2 concentrating mechanism in C3 plants, and the manipulation of photorespiratory bypasses in C3 plants, which are discussed in detail. Improving Rubisco's carboxylation efficiency is possible by engineering targets such as Rubisco subunits, chaperones, and Rubisco activase enzyme activity. Carbon-concentrating mechanisms can be introduced in C3 plants by the adoption of pyrenoid and carboxysomes, which can increase the CO2 concentration around the Rubisco enzyme. Photorespiration is the process by which the fixed carbon is lost through an oxidative process. Different approaches to reduce carbon and nitrogen loss were discussed. Overall, the potential approaches to improve the photosynthetic process and the way forward were discussed in detail.

Strategies for manipulating Rubisco and creating photorespiratory bypass to boost C3 photosynthesis: Prospects on modern crop improvement

Photosynthesis is a process that uses solar energy to fix CO₂ in the air and converts it into sugar, and ultimately powers almost all life activities on the earth. C₃ photosynthesis is the most common form of photosynthesis in crops. Current efforts of increasing crop yields in response to growing global food requirement are mostly focused on improving C₃ photosynthesis. In this review, we summarized the strategies of C₃ photosynthesis improvement in terms of Rubisco properties and photorespiratory limitation. Potential engineered targets include Rubisco subunits and their catalytic sites, Rubisco assembly chaperones, and Rubisco activase. In addition, we reviewed multiple photorespiratory bypasses built by strategies of synthetic biology to reduce the release of CO₂ and ammonia and minimize energy consumption by photorespiration. The potential strategies are suggested to enhance C₃ photosynthesis and boost crop production.

Comparative Ecophysiology of Black Spruce between Lichen Woodlands and Feathermoss Stands in Eastern Canada

Climate change is likely to affect the growth, development and regeneration of the black spruce stands across the boreal forest. Regeneration failures cause gaps in the dense black spruce-feathermoss (SM) mosaic increasing the landscape proportion of open lichen woodland (LW). The aims of the study are to determine whether the contrasting characteristics of SM and LW induce different maximum carboxylation rate (Vcmax), maximum electron transport rate (Jmax) and light-saturated maximum photosynthesis (Amax) in black spruce trees across a latitudinal or seasonal gradient. Results show that the Vcmax and Jmax were higher in SM than in LW in western Quebec, at the ecotone of the closed-crown and open forest. Vcmax and Jmax were different between SM and LW mainly because nutrient acquisition seems different between stand types. Latitude affects values of Vcmax and Jmax, but the effect could be explained by soil and vegetation composition between experimental plots rather than by latitude. Physiological capacities do not match Amax values for stand types and latitude. Indeed, Amax rates suggest that black spruce in LWs perform as well as those in SMs at the needle scale because Amax would be limited by CO2 concentration which prevents saturation of Rubisco. Despite the lack of difference between the Amax of SM and LW stands, future increases in CO2 concentration and temperature could induce a gap between their respective photosynthesis rates because of their different physiological capacities.

Investigation of carbon and energy metabolic mechanism of mixotrophy in Chromochloris zofingiensis

BACKGROUND

Mixotrophy can confer a higher growth rate than the sum of photoautotrophy and heterotrophy in many microalgal species. Thus, it has been applied to biodiesel production and wastewater utilization. However, its carbon and energy metabolic mechanism is currently poorly understood.

RESULTS

To elucidate underlying carbon and energy metabolic mechanism of mixotrophy, Chromochloris zofingiensis was employed in the present study. Photosynthesis and glucose metabolism were found to operate in a dynamic balance during mixotrophic cultivation, the enhancement of one led to the lowering of the other. Furthermore, compared with photoautotrophy, non-photochemical quenching and photorespiration, considered by many as energy dissipation processes, were significantly reduced under mixotrophy. Comparative transcriptome analysis suggested that the intermediates of glycolysis could directly enter the chloroplast and replace RuBisCO-fixed CO₂ to provide carbon sources for chloroplast organic carbon metabolism under mixotrophy. Therefore, the photosynthesis rate-limiting enzyme, RuBisCO, was skipped, allowing for more efficient utilization of photoreaction-derived energy. Besides, compared with heterotrophy, photoreaction-derived ATP reduced the need for TCA-derived ATP, so the glucose decomposition was reduced, which led to higher biomass yield on glucose. Based on these results, a mixotrophic metabolic mechanism was identified.

CONCLUSIONS

Our results demonstrate that the intermediates of glycolysis could directly enter the chloroplast and replace RuBisCO-fixed CO₂ to provide carbon for photosynthesis in mixotrophy. Therefore, the photosynthesis rate-limiting enzyme, RuBisCO, was skipped in mixotrophy, which could reduce energy waste of photosynthesis while promote cell growth. This finding provides a foundation for future studies on mixotrophic biomass production and photosynthetic metabolism.

From CO2 activation to catalytic reduction: a metal-free approach

Over exploitation of natural resources and human activities are relentlessly fueling the emission of CO2 in the atmosphere. Accordingly, continuous efforts are required to find solutions to address the issue of excessive CO2 emission and its potential effects on climate change. It is imperative that the world looks towards a portfolio of carbon mitigation solutions, rather than a single strategy. In this regard, the use of CO2 as a C1 source is an attractive strategy as CO2 has the potential to be a great asset for the industrial sector and consumers across the globe. In particular, the reduction of CO2 offers an alternative to fossil fuels for various organic industrial feedstocks and fuels. Consequently, efficient and scalable approaches for the reduction of CO2 to products such as methane and methanol can generate value from its emissions. Accordingly, in recent years, metal-free catalysis has emerged as a sustainable approach because of the mild reaction conditions by which CO2 can be reduced to various value-added products. The metal-free catalytic reduction of CO2 offers the development of chemical processes with low cost, earth-abundant, non-toxic reagents, and low carbon-footprint. Thus, this perspective aims to present the developments in both the reduction and reductive functionalization chemistry of CO2 during the last decade using various metal-free catalysts.

Continuous artificial synthesis of glucose precursor using enzyme-immobilized microfluidic reactors

Food production in green crops is severely limited by low activity and poor specificity of D-ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) in natural photosynthesis (NPS). This work presents a scientific solution to overcome this problem by immobilizing RuBisCO into a microfluidic reactor, which demonstrates a continuous production of glucose precursor at 13.8 μmol g⁻¹ RuBisCO min⁻¹ from CO₂ and ribulose-1,5-bisphosphate. Experiments show that the RuBisCO immobilization significantly enhances enzyme stabilities (7.2 folds in storage stability, 6.7 folds in thermal stability), and also improves the reusability (90.4% activity retained after 5 cycles of reuse and 78.5% after 10 cycles). This work mimics the NPS pathway with scalable microreactors for continuous synthesis of glucose precursor using very small amount of RuBisCO. Although still far from industrial production, this work demonstrates artificial synthesis of basic food materials by replicating the light-independent reactions of NPS, which may hold the key to food crisis relief and future space colonization.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a difficult enzyme to work with. Here, the authors covalently immobilized it in a microfluidic reactor to enhance its storage/thermal stabilities and reusability, which enabled the continuous artificial synthesis of glucose precursor.

Transition Metal-Free CO2 Fixation into New Carbon-Carbon Bonds

CO₂ is the ultimate renewable carbon source on Earth and the essential C₁ building block for carbohydrate biosynthesis in photosynthetic organisms. Modern synthetic chemistry is facing the key challenge of developing fundamental transformations, such as C-C bond formation, in a sustainable and efficient manner from renewable sources. In this Minireview, the most significant methods recently reported for CO₂ fixation under transition metal-free conditions are summarized, organized into three different chapters according to the nature of the chemical transformation that forges the new C-C bond. The focus is on the mechanistic aspects of the different CO₂ activation modes, with specific attention to those systems that operate under catalytic conditions.

Structural Characterization of a Newly Identified Component of α-Carboxysomes: The AAA+ Domain Protein CsoCbbQ

Carboxysomes are bacterial microcompartments that enhance carbon fixation by concentrating ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and its substrate CO2 within a proteinaceous shell. They are found in all cyanobacteria, some purple photoautotrophs and many chemoautotrophic bacteria. Carboxysomes consist of a protein shell that encapsulates several hundred molecules of RuBisCO, and contain carbonic anhydrase and other accessory proteins. Genes coding for carboxysome shell components and the encapsulated proteins are typically found together in an operon. The α-carboxysome operon is embedded in a cluster of additional, conserved genes that are presumably related to its function. In many chemoautotrophs, products of the expanded carboxysome locus include CbbO and CbbQ, a member of the AAA+ domain superfamily. We bioinformatically identified subtypes of CbbQ proteins and show that their genes frequently co-occur with both Form IA and Form II RuBisCO. The α-carboxysome-associated ortholog, CsoCbbQ, from Halothiobacillus neapolitanus forms a hexamer in solution and hydrolyzes ATP. The crystal structure shows that CsoCbbQ is a hexamer of the typical AAA+ domain; the additional C-terminal domain, diagnostic of the CbbQ subfamily, structurally fills the inter-monomer gaps, resulting in a distinctly hexagonal shape. We show that CsoCbbQ interacts with CsoCbbO and is a component of the carboxysome shell, the first example of ATPase activity associated with a bacterial microcompartment.

Structure and mechanism of the Rubisco-assembly chaperone Raf1

Biogenesis of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits, requires assembly chaperones. Here we analyzed the role of Rubisco accumulation factor1 (Raf1), a dimer of ∼40-kDa subunits. We find that Raf1 from Synechococcus elongatus acts downstream of chaperonin-assisted RbcL folding by stabilizing RbcL antiparallel dimers for assembly into RbcL8 complexes with four Raf1 dimers bound. Raf1 displacement by RbcS results in holoenzyme formation. Crystal structures show that Raf1 from Arabidopsis thaliana consists of a β-sheet dimerization domain and a flexibly linked α-helical domain. Chemical cross-linking and EM reconstruction indicate that the β-domains bind along the equator of each RbcL2 unit, and the α-helical domains embrace the top and bottom edges of RbcL2. Raf1 fulfills a role similar to that of the assembly chaperone RbcX, thus suggesting that functionally redundant factors ensure efficient Rubisco biogenesis.

Role of auxiliary proteins in Rubisco biogenesis and function

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the conversion of atmospheric CO2 into organic compounds during photosynthesis. Despite its pivotal role in plant metabolism, Rubisco is an inefficient enzyme and has therefore been a key target in bioengineering efforts to improve crop yields. Much has been learnt about the complex cellular machinery involved in Rubisco assembly and metabolic repair over recent years. The simple form of Rubisco found in certain bacteria and dinoflagellates comprises two large subunits, and generally requires the chaperonin system for folding. However, the evolution of hexadecameric Rubisco, which comprises eight large and eight small subunits, from its dimeric precursor has rendered Rubisco in most plants, algae, cyanobacteria and proteobacteria dependent on an array of additional factors. These auxiliary factors include several chaperones for assembly as well as ATPases of the AAA+ family for functional maintenance. An integrated view of the pathways underlying Rubisco biogenesis and repair will pave the way for efforts to improve the enzyme with the goal of increasing crop yields.

Isolation and kinetic characterisation of hydrophobically distinct populations of form I Rubisco

BACKGROUND

Rubisco (Ribulose-1,5-bisphosphate carboxylase/oxygenase) is a Calvin Cycle enzyme involved in CO2 assimilation. It is thought to be a major cause of photosynthetic inefficiency, suffering from both a slow catalytic rate and lack of specificity due to a competing reaction with oxygen. Revealing and understanding the engineering rules that dictate Rubisco's activity could have a significant impact on photosynthetic efficiency and crop yield.

RESULTS

This paper describes the purification and characterisation of a number of hydrophobically distinct populations of Rubisco from both Spinacia oleracea and Brassica oleracea extracts. The populations were obtained using a novel and rapid purification protocol that employs hydrophobic interaction chromatography (HIC) as a form I Rubisco enrichment procedure, resulting in distinct Rubisco populations of expected enzymatic activities, high purities and integrity.

CONCLUSIONS

We demonstrate here that HIC can be employed to isolate form I Rubisco with purities and activities comparable to those obtained via ion exchange chromatography (IEC). Interestingly, and in contrast to other published purification methods, HIC resulted in the isolation of a number of hydrophobically distinct Rubisco populations. Our findings reveal a so far unaccounted diversity in the hydrophobic properties within form 1 Rubisco. By employing HIC to isolate and characterise Spinacia oleracea and Brassica oleracea, we show that the presence of these distinct Rubisco populations is not species specific, and we report for the first time the kinetic properties of Rubisco from Brassica oleracea extracts. These observations may aid future studies concerning Rubisco's structural and functional properties.

Molecular chaperones are nanomachines that catalytically unfold misfolded and alternatively folded proteins

By virtue of their general ability to bind (hold) translocating or unfolding polypeptides otherwise doomed to aggregate, molecular chaperones are commonly dubbed “holdases”. Yet, chaperones also carry physiological functions that do not necessitate prevention of aggregation, such as altering the native states of proteins, as in the disassembly of SNARE complexes and clathrin coats. To carry such physiological functions, major members of the Hsp70, Hsp110, Hsp100, and Hsp60/CCT chaperone families act as catalytic unfolding enzymes or unfoldases that drive iterative cycles of protein binding, unfolding/pulling, and release. One unfoldase chaperone may thus successively convert many misfolded or alternatively folded polypeptide substrates into transiently unfolded intermediates, which, once released, can spontaneously refold into low-affinity native products. Whereas during stress, a large excess of non-catalytic chaperones in holding mode may optimally prevent protein aggregation, after the stress, catalytic disaggregases and unfoldases may act as nanomachines that use the energy of ATP hydrolysis to repair proteins with compromised conformations. Thus, holding and catalytic unfolding chaperones can act as primary cellular defenses against the formation of early misfolded and aggregated proteotoxic conformers in order to avert or retard the onset of degenerative protein conformational diseases.

Carbonic anhydrases in industrial applications

Carbonic anhydrases (CAs) catalyze a fundamental reaction: the reversible hydration and dehydration of carbon dioxide (CO2) and bicarbonate ([Formula: see text]), respectively. Current methods for CO2 capture and sequestration are harsh, expensive, and require prohibitively large energy inputs, effectively negating the purpose of removing CO2 from the atmosphere. Due to CA's activity on CO2 there is increasing interest in using CAs for industrial applications such as carbon sequestration and biofuel production. A lot of work in the last decade has focused on immobilizing CA onto various supports for incorporation into CO2 scrubbing applications or devices. Although the proof of principle has been validated, current CAs being tested do not withstand the harsh industrial conditions. The advent of large-scale genome sequencing projects has resulted in several emerging efforts seeking out novel CAs from a variety of microorganisms, including bacteria, micro-, and macro-algae. CAs are also being investigated for their use in medical applications, such drug delivery systems and artificial lungs. This review also looks at possible downstream uses of captured and sequestered CO2, from using it to enhance oil recovery to incorporating it into useful and financially viable products.

Engineering photorespiration: current state and future possibilities

Reduction of flux through photorespiration has been viewed as a major way to improve crop carbon fixation and yield since the energy-consuming reactions associated with this pathway were discovered. This view has been supported by the biomasses increases observed in model species that expressed artificial bypass reactions to photorespiration. Here, we present an overview about the major current attempts to reduce photorespiratory losses in crop species and provide suggestions for future research priorities.

Carbonic Anhydrase: An Efficient Enzyme with Possible Global Implications

As the global atmospheric emissions of carbon dioxide (CO2) and other greenhouse gases continue to grow to record-setting levels, so do the demands for an efficient and inexpensive carbon sequestration system. Concurrently, the first-world dependence on crude oil and natural gas provokes concerns for long-term availability and emphasizes the need for alternative fuel sources. At the forefront of both of these research areas are a family of enzymes known as the carbonic anhydrases (CAs), which reversibly catalyze the hydration of CO2into bicarbonate. CAs are among the fastest enzymes known, which have a maximum catalytic efficiency approaching the diffusion limit of 108 M−1s−1. As such, CAs are being utilized in various industrial and research settings to help lower CO2atmospheric emissions and promote biofuel production. This review will highlight some of the recent accomplishments in these areas along with a discussion on their current limitations.

Pulsed magnetic field: a contemporary approach offers to enhance plant growth and yield of soybean

The possible involvement of pulsed magnetic field (PMF) pretreatment in development and yield of soybean was investigated. Seeds were subjected to 20 days with 1500 nT at 10.0 Hz of PMF for 5 h per day. PMF pretreatment increased the plant height, fresh and dry weight, and protein content with the changes of protein profile in 8 days old seedlings. In addition, activity of enzymes such as β-amylase, acid phosphatase, polyphenol oxidase and catalase was enhanced while α-amylase, alkaline phosphatase, protease and nitrate reductase activities declined due to PMF exposure. However, a considerable increment of Fe, Cu, Mn, Zn, Mg, K and Na contents with reduced level of Ca was found in PMF treated seedlings. The number of leaves, pods, seeds and length of pods, and weight of seeds were also remarkably higher in PMF treatment in contrast to controls. The results suggest that pretreatment of PMF plays important roles in improvement of crop productivity of soybean through the enhancement of protein, mineral accumulation and enzyme activities which leads to increase the growth and yield.