Advancing our understanding and capacity to engineer nature's CO2-sequestering enzyme, Rubisco

Introduction of a phenylalanine sink in fast growing cyanobacterium Synechococcus elongatus PCC 11801 leads to improved PSII efficiency, linear electron transport, and carbon fixation

Cyanobacteria are investigated for fundamental photosynthesis research and sustainable production of valuable biochemicals. However, low product titer and biomass productivities are major bottlenecks to the economical scale-up. Recent studies have shown that the introduction of a metabolic sink, such as sucrose, 2,3-butanediol, and 2-phenyl ethanol, in cyanobacteria improves carbon fixation by relieving the "sink" limitation of photosynthesis. However, the impact of light intensity on the behavior of this sink-derived enhancement in carbon fixation is not well understood and is necessary for translation to outdoor cultivation. Here, using random mutagenesis, we engineered Synechococcus elongatus PCC 11801 to overproduce 1.24 g L-1 phenylalanine (Phe) in 3 days, identified L531W in the TolC protein as an important driver of Phe efflux, and investigated the effect of light intensity on total carbon fixation. We found that low light results in competition between biomass and Phe, whereas under excess light, a higher flux of fixed carbon is directed to the Phe sink. The introduction of the Phe sink improves the quantum yields of photosystem I and II with a concomitant increase in the total electron flow leading to nearly 70% increase in carbon fixation at high light in the mutant strain. Additionally, the cyclic electron flow decreased, which has implications for the ATP/NADPH production ratio. Our data highlight how light intensity affects the sink-derived enhancement in carbon fixation, the role of CEF to balance the source-sink demand for ATP and NADPH, and the enhancement of inorganic carbon fixation in cyanobacteria with an engineered sink.

Engineering Rubisco condensation in chloroplasts to manipulate plant photosynthesis

Although Rubisco is the most abundant enzyme globally, it is inefficient for carbon fixation because of its low turnover rate and limited ability to distinguish CO2 and O2, especially under high O2 conditions. To address these limitations, phytoplankton, including cyanobacteria and algae, have evolved CO2-concentrating mechanisms (CCM) that involve compartmentalizing Rubisco within specific structures, such as carboxysomes in cyanobacteria or pyrenoids in algae. Engineering plant chloroplasts to establish similar structures for compartmentalizing Rubisco has attracted increasing interest for improving photosynthesis and carbon assimilation in crop plants. Here, we present a method to effectively induce the condensation of endogenous Rubisco within tobacco (Nicotiana tabacum) chloroplasts by genetically fusing superfolder green fluorescent protein (sfGFP) to the tobacco Rubisco large subunit (RbcL). By leveraging the intrinsic oligomerization feature of sfGFP, we successfully created pyrenoid-like Rubisco condensates that display dynamic, liquid-like properties within chloroplasts without affecting Rubisco assembly and catalytic function. The transgenic tobacco plants demonstrated comparable autotrophic growth rates and full life cycles in ambient air relative to the wild-type plants. Our study offers a promising strategy for modulating endogenous Rubisco assembly and spatial organization in plant chloroplasts via phase separation, which provides the foundation for generating synthetic organelle-like structures for carbon fixation, such as carboxysomes and pyrenoids, to optimize photosynthetic efficiency.

Engineering CO2-fixing modules in Escherichia coli via efficient assembly of cyanobacterial Rubisco and carboxysomes

Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) is the central enzyme for conversion of atmospheric CO2 into organic molecules, playing a crucial role in the global carbon cycle. In cyanobacteria and some chemoautotrophs, Rubisco complexes, together with carbonic anhydrase, are enclosed within specific proteinaceous microcompartments known as carboxysomes. The polyhedral carboxysome shell ensures the dense packaging of Rubisco and creates a high-CO2 internal environment to facilitate CO2 fixation. Rubisco and carboxysomes have been popular targets for bioengineering, with the intent of enhancing plant photosynthesis, crop yields, and biofuel production. However, efficient generation of Form 1B Rubisco and cyanobacterial β-carboxysomes in heterologous systems remains a challenge. Here, we developed genetic systems to efficiently engineer functional cyanobacterial Form 1B Rubisco in Escherichia coli by incorporating Rubisco assembly factor Raf1 and modulating the RbcL/S stoichiometry. We then reconstituted catalytically active β-carboxysomes in E. coli with cognate Form 1B Rubisco by fine-tuning the expression levels of individual β-carboxysome components. In addition, we investigated the mechanism of Rubisco encapsulation into carboxysomes by constructing hybrid carboxysomes; this was achieved by creating a chimeric encapsulation peptide incorporating small sub-unit-like domains, which enabled the encapsulation of Form 1B Rubisco into α-carboxysome shells. Our study provides insights into the assembly mechanisms of plant-like Form 1B Rubisco and the principles of its encapsulation in both β-carboxysomes and hybrid carboxysomes, highlighting the inherent modularity of carboxysome structures. These findings lay the framework for rational design and repurposing of CO2-fixing modules in bioengineering applications, e.g., crop engineering, biocatalyst production, and molecule delivery.

Enzymatic and quantitative properties of Rubisco in some conifers and lycopods

Information on the kinetic properties of Rubisco, a key enzyme for photosynthesis, is scarce in land plants that emerged early during the evolutionary process. This study examined the carboxylase activity and abundance of Rubisco in five conifers, two lycopods, and three control C3 crops. The turnover rates of Rubisco carboxylation (kcatc) under saturated-CO2 conditions in conifers and lycopods were comparable to those in the control C3 crops. Rubisco carboxylase activity under CO2-unsaturated conditions (vcu) was also measured using reaction mixtures saturated with a N2 gas containing CO2 and O2 at present atmospheric levels to predict the Rubisco CO2 affinity from the percentage of vcu in kcatc. The predicted CO2 affinity in conifers and lycopods tended to be lower than that in the control C3 crops. When the control C3 crops and two previously examined C4 crops were analyzed together, the kcatc of Rubisco with a low CO2 affinity tended to be high. N allocation to Rubisco with a low kcatc tended to be high in these plants. In conifers and lycopods, the kcatc was lower than that expected on the basis of predicted Rubisco CO2 affinity, unlike in the control crops. N allocation to Rubisco also tended to be lower than that expected on the basis of kcatc. These results indicate that Rubisco in the examined conifers and lycopods is not superior in terms of both kcatc and CO2 affinity and that the abundance of Rubisco is not necessarily closely related to its kinetic properties. The reason for these phenomena is discussed in terms of the molecular evolution of Rubisco.

Towards carbon neutrality: Enhancing CO2 sequestration by plants to reduce carbon footprint

To achieve carbon neutrality and address climate change effectively, strategies emphasizing plant-based CO2 sequestration are essential. This research integrates process optimization, sustainable practices, and technological innovations to augment plants' natural CO2 absorption, thereby enhancing ecosystem carbon storage and aiding in greenhouse gas (GHG) mitigation. The study highlights the critical role of merging process integration with sustainable farming, precision agriculture, and bioengineering to enhance CO2 sequestration. The research emphasizes employing Life Cycle Assessment (LCA) and Carbon Footprint Analysis (CFA) as vital tools for quantifying CO2 sequestration strategies' environmental benefits and effectiveness, ensuring a comprehensive approach to cleaner production and waste management. By examining case studies and models, this research assesses the contribution of these approaches to reducing carbon footprints and advancing towards carbon neutrality. The findings advocate for a cohesive strategy that blends technological advancements with sustainable agricultural practices, aimed at reducing global carbon emissions and achieving carbon neutrality.

Rubisco packaging and stoichiometric composition of the native β-carboxysome in Synechococcus elongatus PCC7942

Carboxysomes are anabolic bacterial microcompartments that play an essential role in CO2 fixation in cyanobacteria. This self-assembling proteinaceous organelle uses a polyhedral shell constructed by hundreds of shell protein paralogs to encapsulate the key CO2-fixing enzymes Rubisco and carbonic anhydrase. Deciphering the precise arrangement and structural organization of Rubisco enzymes within carboxysomes is crucial for understanding carboxysome formation and overall functionality. Here, we employed cryoelectron tomography and subtomogram averaging to delineate the 3D packaging of Rubiscos within β-carboxysomes in the freshwater cyanobacterium Synechococcus elongatus PCC7942 grown under low light. Our results revealed that Rubiscos are arranged in multiple concentric layers parallel to the shell within the β-carboxysome lumen. We also detected Rubisco binding with the scaffolding protein CcmM in β-carboxysomes, which is instrumental for Rubisco encapsulation and β-carboxysome assembly. Using Quantification conCATamer-based quantitative MS, we determined the absolute stoichiometric composition of the entire β-carboxysome. This study provides insights into the assembly principles and structural variation of β-carboxysomes, which will aid in the rational design and repurposing of carboxysome nanostructures for diverse bioengineering applications.

Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms

Rose is an important ornamental crop cultivated globally for perfume production. However, our understanding of the mechanisms underlying scent production and molecular breeding for fragrance is hindered by the lack of a reference genome for tea roses. We present the first complete telomere-to-telomere (T2T) genome of Rosa gigantea, with high quality (QV > 60), including detailed characterization of the structural features of repetitive regions. The expansion of genes associated with phenylpropanoid biosynthesis may account for the unique tea scent. We uncover the release rhythm of aromatic volatile organic compounds and their gene regulatory networks through comparative genomics and time-ordered gene co-expression networks. Analyzes of eugenol homologs demonstrate how plants attract pollinators using specialized phenylpropanoids in specific tissues. This study highlights the conservation and utilization of genetic diversity from wild endangered species through multi-omics approaches, providing a scientific foundation for enhancing rose fragrance via de novo domestication.

Functional Analysis of the PoSERK-Interacting Protein PorbcL in the Embryogenic Callus Formation of Tree Peony (Paeonia ostii T. Hong et J. X. Zhang)

SERK is a marker gene for early somatic embryogenesis. We screened and functionally verified a SERK-interacting protein to gain insights into tree-peony somatic embryogenesis. Using PoSERK as bait, we identified PorbcL (i.e., the large subunit of Rubisco) as a SERK-interacting protein from a yeast two-hybrid (Y2H) library of cDNA from developing tree-peony somatic embryos. The interaction between PorbcL and PoSERK was verified by Y2H and bimolecular fluorescence complementation analyses. PorbcL encodes a 586-amino-acid acidic non-secreted hydrophobic non-transmembrane protein that is mainly localized in the chloroplast and plasma membrane. PorbcL was highly expressed in tree-peony roots and flowers and was up-regulated during zygotic embryo development. PorbcL overexpression caused the up-regulation of PoSERK (encoding somatic embryogenesis receptor-like kinase), PoAGL15 (encoding agamous-like 15), and PoGPT1 (encoding glucose-6-phosphate translocator), while it caused the down-regulation of PoLEC1 (encoding leafy cotyledon 1) in tree-peony callus. PorbcL overexpression led to increased indole-3-acetic acid (IAA) content but decreasing contents of abscisic acid (ABA) and 6-benzyladenosine (BAPR). The changes in gene expression, high IAA levels, and increased ratio of IAA to ABA, BAPR, 1-Aminocyclopropanecarboxylic acid (ACC), 5-Deoxystrigol (5DS), and brassinolide (BL) promoted embryogenesis. These results provide a foundation for establishing a tree-peony embryogenic callus system.

Rubisco kinetic adaptations to extreme environments

Photosynthetic and chemosynthetic extremophiles have evolved adaptations to thrive in challenging environments by finely adjusting their metabolic pathways through evolutionary processes. A prime adaptation target to allow autotrophy in extreme conditions is the enzyme Rubisco, which plays a central role in the conversion of inorganic to organic carbon. Here, we present an extensive compilation of Rubisco kinetic traits from a wide range of species of bacteria, archaea, algae, and plants, sorted by phylogenetic group, Rubisco type, and extremophile type. Our results show that Rubisco kinetics for the few extremophile organisms reported up to date are placed at the margins of the enzyme's natural variability. Form ID Rubisco from thermoacidophile rhodophytes and form IB Rubisco from halophile terrestrial plants exhibit higher specificity and affinity for CO2 than their non-extremophilic counterparts, as well as higher carboxylation efficiency, whereas form ID Rubisco from psychrophile organisms possess lower affinity for O2. Additionally, form IB Rubisco from thermophile cyanobacteria shows enhanced CO2 specificity when compared to form IB non-extremophilic cyanobacteria. Overall, these findings highlight the unique characteristics of extremophile Rubisco enzymes and provide useful clues to guide next explorations aimed at finding more efficient Rubiscos.

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.

Tailoring regulatory components for metabolic engineering in cyanobacteria

The looming climate crisis has prompted an ever-growing interest in cyanobacteria due to their potential as sustainable production platforms for the synthesis of energy carriers and value-added chemicals from CO2 and sunlight. Nonetheless, cyanobacteria are yet to compete with heterotrophic systems in terms of space-time yields and consequently production costs. One major drawback leading to the low production performance observed in cyanobacteria is the limited ability to utilize the full capacity of the photosynthetic apparatus and its associated systems, i.e. CO2 fixation and the directly connected metabolism. In this review, novel insights into various levels of metabolic regulation of cyanobacteria are discussed, including the potential of targeting these regulatory mechanisms to create a chassis with a phenotype favorable for photoautotrophic production. Compared to conventional metabolic engineering approaches, minor perturbations of regulatory mechanisms can have wide-ranging effects.

A carboxysome-based CO2 concentrating mechanism for C3 crop chloroplasts: advances and the road ahead

The introduction of the carboxysome-based CO2 concentrating mechanism (CCM) into crop plants has been modelled to significantly increase crop yields. This projection serves as motivation for pursuing this strategy to contribute to global food security. The successful implementation of this engineering challenge is reliant upon the transfer of a microcompartment that encapsulates cyanobacterial Rubisco, known as the carboxysome, alongside active bicarbonate transporters. To date, significant progress has been achieved with respect to understanding various aspects of the cyanobacterial CCM, and more recently, different components of the carboxysome have been successfully introduced into plant chloroplasts. In this Perspective piece, we summarise recent findings and offer new research avenues that will accelerate research in this field to ultimately and successfully introduce the carboxysome into crop plants for increased crop yields.

Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus

Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self-assembly principles of the intact carboxysome remain elusive. Here we purified α-carboxysomes from Prochlorococcus and examined their intact structures using single-particle cryo-electron microscopy to solve the basic principles of their shell construction and internal RuBisCO organization. The 4.2 Å icosahedral-like shell structure reveals 24 CsoS1 hexamers on each facet and one CsoS4A pentamer at each vertex. RuBisCOs are organized into three concentric layers within the shell, consisting of 72, 32 and up to 4 RuBisCOs at the outer, middle and inner layers, respectively. We uniquely show how full-length and shorter forms of the scaffolding protein CsoS2 bind to the inner surface of the shell via repetitive motifs in the middle and C-terminal regions. Combined with previous reports, we propose a concomitant 'outside-in' assembly principle of α-carboxysomes: the inner surface of the self-assembled shell is reinforced by the middle and C-terminal motifs of the scaffolding protein, while the free N-terminal motifs cluster to recruit RuBisCO in concentric, three-layered spherical arrangements. These new insights into the coordinated assembly of α-carboxysomes may guide the rational design and repurposing of carboxysome structures for improving plant photosynthetic efficiency.

Knocking Out Chloroplastic Aldolases/Rubisco Lysine Methyltransferase Enhances Biomass Accumulation in Nannochloropsis oceanica under High-Light Stress

Rubisco large-subunit methyltransferase (LSMT), a SET-domain protein lysine methyltransferase, catalyzes the formation of trimethyl-lysine in the large subunit of Rubisco or in fructose-1,6-bisphosphate aldolases (FBAs). Rubisco and FBAs are both vital proteins involved in CO2 fixation in chloroplasts; however, the physiological effect of their trimethylation remains unknown. In Nannochloropsis oceanica, a homolog of LSMT (NoLSMT) is found. Phylogenetic analysis indicates that NoLSMT and other algae LSMTs are clustered in a basal position, suggesting that algal species are the origin of LSMT. As NoLSMT lacks the His-Ala/ProTrp triad, it is predicted to have FBAs as its substrate instead of Rubisco. The 18-20% reduced abundance of FBA methylation in NoLSMT-defective mutants further confirms this observation. Moreover, this gene (nolsmt) can be induced by low-CO2 conditions. Intriguingly, NoLSMT-knockout N. oceanica mutants exhibit a 9.7-13.8% increase in dry weight and enhanced growth, which is attributed to the alleviation of photoinhibition under high-light stress. This suggests that the elimination of FBA trimethylation facilitates carbon fixation under high-light stress conditions. These findings have implications in engineering carbon fixation to improve microalgae biomass production.

Rubisco is evolving for improved catalytic efficiency and CO2 assimilation in plants

Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of the molecular and kinetic evolution of Form I rubisco we uncover the evolutionary trajectory of rubisco kinetic evolution in angiosperms. We show that rbcL is among the 1% of slowest-evolving genes and enzymes on Earth, accumulating one nucleotide substitution every 0.9 My and one amino acid mutation every 7.2 My. Despite this, rubisco catalysis has been continually evolving toward improved CO2/O2 specificity, carboxylase turnover, and carboxylation efficiency. Consistent with this kinetic adaptation, increased rubisco evolution has led to a concomitant improvement in leaf-level CO2 assimilation. Thus, rubisco has been slowly but continually evolving toward improved catalytic efficiency and CO2 assimilation in plants.

Engineering Rubisco to enhance CO2 utilization

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a pivotal enzyme that mediates the fixation of CO2. As the most abundant protein on earth, Rubisco has a significant impact on global carbon, water, and nitrogen cycles. However, the significantly low carboxylation activity and competing oxygenase activity of Rubisco greatly impede high carbon fixation efficiency. This review first summarizes the current efforts in directly or indirectly modifying plant Rubisco, which has been challenging due to its high conservation and limitations in chloroplast transformation techniques. However, recent advancements in understanding Rubisco biogenesis with the assistance of chaperones have enabled successful heterologous expression of all Rubisco forms, including plant Rubisco, in microorganisms. This breakthrough facilitates the acquisition and evaluation of modified proteins, streamlining the measurement of their activity. Moreover, the establishment of a screening system in E. coli opens up possibilities for obtaining high-performance mutant enzymes through directed evolution. Finally, this review emphasizes the utilization of Rubisco in microorganisms, not only expanding their carbon-fixing capabilities but also holding significant potential for enhancing biotransformation processes.

Equisetum praealtum and E. hyemale have abundant Rubisco with a high catalytic turnover rate and low CO2 affinity

The kinetic properties of Rubisco, a key enzyme for photosynthesis, have been examined in numerous plant species. However, this information on some plant groups, such as ferns, is scarce. This study examined Rubisco carboxylase activity and leaf Rubisco levels in seven ferns, including four Equisetum plants (E. arvense, E. hyemale, E. praealtum, and E. variegatum), considered living fossils. The turnover rates of Rubisco carboxylation (kcatc) in E. praealtum and E. hyemale were comparable to those in the C4 plants maize (Zea mays) and sorghum (Sorghum bicolor), whose kcatc values are high. Rubisco CO2 affinity, estimated from the percentage of Rubisco carboxylase activity under CO2 unsaturated conditions in kcatc in these Equisetum plants, was low and also comparable to that in maize and sorghum. In contrast, kcatc and CO2 affinities of Rubisco in other ferns, including E. arvense and E. variegatum were comparable with those in C3 plants. The N allocation to Rubisco in the ferns examined was comparable to that in the C3 plants. These results indicate that E. praealtum and E. hyemale have abundant Rubisco with high kcatc and low CO2 affinity, whereas the carboxylase activity and abundance of Rubisco in other ferns were similar to those in C3 plants. Herein, the Rubisco properties of E. praealtum and E. hyemale were discussed regarding their evolution and physiological implications.

Bio-Inspired Microreactors Continuously Synthesize Glucose Precursor from CO2 with an Energy Conversion Efficiency 3.3 Times of Rice

Excessive CO2 and food shortage are two grand challenges of human society. Directly converting CO2 into food materials can simultaneously alleviate both, like what green crops do in nature. Nevertheless, natural photosynthesis has a limited energy efficiency due to low activity and specificity of key enzyme D-ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). To enhance the efficiency, many prior studies focused on engineering the enzymes, but this study chooses to learn from the nature to design more efficient reactors. This work is original in mimicking the stacked structure of thylakoids in chloroplasts to immobilize RuBisCO in a microreactor using the layer-by-layer strategy, obtaining the continuous conversion of CO2 into glucose precursor at 1.9 nmol min-1 with enhanced activity (1.5 times), stability (≈8 times), and reusability (96% after 10 reuses) relative to the free RuBisCO. The microreactors are further scaled out from one to six in parallel and achieve the production at 15.8 nmol min-1 with an energy conversion efficiency of 3.3 times of rice, showing better performance of this artificial synthesis than NPS in terms of energy conversion efficiency. The exploration of the potential of mass production would benefit both food supply and carbon neutralization.

Regulation of photosynthesis by mitogen-activated protein kinase in rice: antagonistic adjustment by OsMPK3 and OsMPK6

Photosynthesis is the basis of almost all life on earth and is the main component of crop yield that contributes to the carbohydrate partitioning to the grains. Maintaining the photosynthetic efficiency of plants in challenging environmental conditions by regulating the associated factors is a potential research arena which will help in the improvement of crop yield. Phosphorylation is known to play a pivotal role in the regulation of photosynthesis. Mitogen Activated Protein Kinases (MAPKs) cascade although known to regulate a diverse range of processes does not have any exact reported function in the regulation of photosynthesis. To elucidate the regulatory role of MAPKs in photosynthesis we investigated the changes in net photosynthesis rate and related parameters in DEX inducible over-expressing (OE) lines of two members of MAPK gene family namely, OsMPK3 and OsMPK6 in rice. Interestingly, significant changes were found in net photosynthesis rate and related physiological parameters in OsMPK3 and OsMPK6-OE lines compared to its wild-type relatives. OsMPK3 and OsMPK6 have regulatory effects on nuclear-encoded photosynthetic genes. Untargeted metabolite profiling reveals a higher accumulation of sugars and their derivatives in MPK6 overexpressing plants and a lower accumulation of sugars and organic acids in MPK3 overexpressing plants. The accumulation of amino acids was found in abundance in both MPK3 and MPK6 overexpressing plants. Understanding the effects of MPK3 and MPK6 on the CO2 assimilation of rice plants under normal growth conditions, will help in devising strategies that can be extended for crop improvement.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01383-9.

The pyrenoid: the eukaryotic CO2-concentrating organelle

The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.

Leaf physiological and morphological constraints of water-use efficiency in C3 plants

The increasing evaporative demand due to climate change will significantly affect the balance of carbon assimilation and water losses of plants worldwide. The development of crop varieties with improved water-use efficiency (WUE) will be critical for adapting agricultural strategies under predicted future climates. This review aims to summarize the most important leaf morpho-physiological constraints of WUE in C3 plants and identify gaps in knowledge. From the carbon gain side of the WUE, the discussed parameters are mesophyll conductance, carboxylation efficiency and respiratory losses. The traits and parameters affecting the waterside of WUE balance discussed in this review are stomatal size and density, stomatal control and residual water losses (cuticular and bark conductance), nocturnal conductance and leaf hydraulic conductance. In addition, we discussed the impact of leaf anatomy and crown architecture on both the carbon gain and water loss components of WUE. There are multiple possible targets for future development in understanding sources of WUE variability in plants. We identified residual water losses and respiratory carbon losses as the greatest knowledge gaps of whole-plant WUE assessments. Moreover, the impact of trichomes, leaf hydraulic conductance and canopy structure on plants' WUE is still not well understood. The development of a multi-trait approach is urgently needed for a better understanding of WUE dynamics and optimization.

Temperature sensitivity of carbon concentrating mechanisms in the diatom Phaeodactylum tricornutum

Marine diatoms are key primary producers across diverse habitats in the global ocean. Diatoms rely on a biophysical carbon concentrating mechanism (CCM) to supply high concentrations of CO₂ around their carboxylating enzyme, RuBisCO. The necessity and energetic cost of the CCM are likely to be highly sensitive to temperature, as temperature impacts CO₂ concentration, diffusivity, and the kinetics of CCM components. Here, we used membrane inlet mass spectrometry (MIMS) and modeling to capture temperature regulation of the CCM in the diatom Phaeodactylum tricornutum (Pt). We found that enhanced carbon fixation rates by Pt at elevated temperatures were accompanied by increased CCM activity capable of maintaining RuBisCO close to CO₂ saturation but that the mechanism varied. At 10 and 18 °C, diffusion of CO₂ into the cell, driven by Pt's 'chloroplast pump' was the major inorganic carbon source. However, at 18 °C, upregulation of the chloroplast pump enhanced (while retaining the proportion of) both diffusive CO₂ and active HCO₃^- uptake into the cytosol, and significantly increased chloroplast HCO₃^- concentrations. In contrast, at 25 °C, compared to 18 °C, the chloroplast pump had only a slight increase in activity. While diffusive uptake of CO₂ into the cell remained constant, active HCO₃^- uptake across the cell membrane increased resulting in Pt depending equally on both CO₂ and HCO₃^- as inorganic carbon sources. Despite changes in the CCM, the overall rate of active carbon transport remained double that of carbon fixation across all temperatures tested. The implication of the energetic cost of the Pt CCM in response to increasing temperatures was discussed.

Analysis of photosynthetic pigments pathway produced by CO2-toxicity-induced Scenedesmus obliquus

The coal-to-gas process produces carbon dioxide, which increases global warming, and its wastewater treatment generates sludge with high organic toxicity. Scenedesmus obliquus is a potential solution to such environmental problems, and photosynthetic pigments are the focus of this study. The optimal concentration of CO₂ for the growth of Scenedesmus obliquus was found to be 30 % after increasing the concentration of CO₂ (0.05 %-100 %). The accumulation of photosynthetic pigments during cultivation could reach 31.74 ± 1.33 mg/L, 11.21 ± 0.42 mg/L, and 5.59 ± 0.19 mg/L respectively, and the organic toxicity of sludge extract could be reduced by 44.97 %. Upregulation of A0A383VSL5, A0A383WMQ3, and A0A2Z4THB7 as photo systemic oxygen release proteins and propylene phosphate isomerase resulted in oxygen-evolving proteins in photosystem II, electron transport in photosystem I, and intermediates in carbon fixation. This is achieved by increasing the intracellular antennae protein and carbon fixation pathway, allowing Scenedesmus obliquus to both tolerate and fix CO₂ and reduce the organic toxicity of sludge. These findings provide insights into the innovative strategy underlining the fixation of CO₂, treatment and disposal of industrial residual sludge, and the enhancement of microalgal biomass production.

What can hornworts teach us?

The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.

Variation in Photosynthetic Efficiency under Fluctuating Light between Rose Cultivars and its Potential for Improving Dynamic Photosynthesis

Photosynthetic efficiency under both steady-state and fluctuating light can significantly affect plant growth under naturally fluctuating light conditions. However, the difference in photosynthetic performance between different rose genotypes is little known. This study compared the photosynthetic performance under steady-state and fluctuating light in two modern rose cultivars (Rose hybrida), "Orange Reeva" and "Gelato", and an old Chinese rose plant Rosa chinensis cultivar, "Slater's crimson China". The light and CO₂ response curves indicated that they showed similar photosynthetic capacity under steady state. The light-saturated steady-state photosynthesis in these three rose genotypes was mainly limited by biochemistry (60%) rather than diffusional conductance. Under fluctuating light conditions (alternated between 100 and 1500 μmol photons m^-2 m^-1 every 5 min), stomatal conductance gradually decreased in these three rose genotypes, while mesophyll conductance (g_m) was maintained stable in Orange Reeva and Gelato but decreased by 23% in R. chinensis, resulting in a stronger loss of CO₂ assimilation under high-light phases in R. chinensis (25%) than in Orange Reeva and Gelato (13%). As a result, the variation in photosynthetic efficiency under fluctuating light among rose cultivars was tightly related to g_m. These results highlight the importance of g_m in dynamic photosynthesis and provide new traits for improving photosynthetic efficiency in rose cultivars.

Carbon assimilation in upper subtidal macroalgae is determined by an inverse correlation between Rubisco carboxylation efficiency and CO2 concentrating mechanism effectiveness

Seaweeds have a wide ecophysiological and phylogenetic diversity with species expressing different Rubisco forms that frequently coexist with biophysical CO₂ concentrating mechanisms (CCMs), an adaptation that overcomes the low CO₂ availability and gas diffusion in seawater. Here, we assess the possible coevolution between the Rubisco catalysis and the type and effectiveness of CCMs present in six upper subtidal macroalgal species belonging to three phylogenetic groups of seaweeds. A wide diversity in the Rubisco kinetic traits was found across the analyzed species, although the specificity factor was the only parameter explained by the expressed Rubisco form. Differences in the catalytic trade-offs were found between Rubisco forms, indicating that ID Rubiscos could be better adapted to the intracellular O₂  : CO₂ ratio found in marine organisms during steady-state photosynthesis. The biophysical components of the CCMs also differed among macroalgal species, resulting in different effectiveness to concentrate CO₂ around Rubisco active sites. Interestingly, an inverse relationship was found between the effectiveness of CCMs and the in vitro Rubisco carboxylation efficiency, which possibly led to a similar carboxylation potential across the analyzed macroalgal species. Our results demonstrate a coevolution between Rubisco kinetics and CCMs across phylogenetically distant marine macroalgal species sharing the same environment.

Nuclear-encoded CbbX located in chloroplast is essential for the activity of red-type Rubisco in Saccharina japonica

Saccharina japonica (Laminariales, Phaeophyta) is a brown alga and the major component of algae beds on the northwest coast of the Pacific Ocean. Rubisco, the key enzyme of CO2 fixation in photosynthesis, is inhibited by nonproductive binding of its substrate RuBP and other sugar phosphates. The inhibited Rubisco in eukaryotic phytoplankton of the red plastid lineage was reactivated by CbbXs, the red-type Rubisco activases, through the process of ATP-hydrolysis-powered remodeling. As well documented, CbbXs had two types of subunits encoded by the plastid or nuclear genome respectively. In this study, both proteins of S. japonica (SjCbbX-n and SjCbbX-p) were localized in the chloroplast illustrated by immuno-electron microscopy technique. GST pull-down detection verified SjCbbX-n could interact with SjCbbX-p. Two-dimensional electrophoresis-based Western blot analysis illustrated that the endogenous SjCbbXs could form heterohexamer in the ratio of 1:1. Activase activity assays showed that although both the recombinant proteins of SjCbbXs were functional, SjCbbX-n illustrated the significantly higher activase activity than SjCbbX-p. Notably, when the two proteins were mixed, the highest specific efficiencies of Rubisco were obtained. These results implied SjCbbX-n may be essential for Rubisco activation. Molecular evolutionary analysis of cbbx genes revealed that cbbx-n originated from the duplication of cbbx-p and then evolved independently under the positive selection pressure. This is the first report about the functional relationship between the two types of CbbXs in macroalge with the red-type Rubisco and provides useful information for revealing the mechanism of high photosynthetic efficiency of this important kelp.

Chitosan-Modified Polyethyleneimine Nanoparticles for Enhancing the Carboxylation Reaction and Plants' CO2 Uptake

Increasing plants' photosynthetic efficiency is a major challenge that must be addressed in order to cover the food demands of the growing population in the changing climate. Photosynthesis is greatly limited at the initial carboxylation reaction, where CO₂ is converted to the organic acid 3-PGA, catalyzed by the RuBisCO enzyme. RuBisCO has poor affinity for CO₂, but also the CO₂ concentration at the RuBisCO site is limited by the diffusion of atmospheric CO₂ through the various leaf compartments to the reaction site. Beyond genetic engineering, nanotechnology can offer a materials-based approach for enhancing photosynthesis, and yet, it has mostly been explored for the light-dependent reactions. In this work, we developed polyethyleneimine-based nanoparticles for enhancing the carboxylation reaction. We demonstrate that the nanoparticles can capture CO₂ in the form of bicarbonate and increase the CO₂ that reacts with the RuBisCO enzyme, enhancing the 3-PGA production in in vitro assays by 20%. The nanoparticles can be introduced to the plant via leaf infiltration and, because of the functionalization with chitosan oligomers, they do not induce any toxic effect to the plant. In the leaves, the nanoparticles localize in the apoplastic space but also spontaneously reach the chloroplasts where photosynthetic activity takes place. Their CO₂ loading-dependent fluorescence verifies that, in vivo, they maintain their ability to capture CO₂ and can be therefore reloaded with atmospheric CO₂ while in planta. Our results contribute to the development of a nanomaterials-based CO₂-concentrating mechanism in plants that can potentially increase photosynthetic efficiency and overall plants' CO₂ storage.

Producing fast and active Rubisco in tobacco to enhance photosynthesis

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) performs most of the carbon fixation on Earth. However, plant Rubisco is an intrinsically inefficient enzyme given its low carboxylation rate, representing a major limitation to photosynthesis. Replacing endogenous plant Rubisco with a faster Rubisco is anticipated to enhance crop photosynthesis and productivity. However, the requirement of chaperones for Rubisco expression and assembly has obstructed the efficient production of functional foreign Rubisco in chloroplasts. Here, we report the engineering of a Form 1A Rubisco from the proteobacterium Halothiobacillus neapolitanus in Escherichia coli and tobacco (Nicotiana tabacum) chloroplasts without any cognate chaperones. The native tobacco gene encoding Rubisco large subunit was genetically replaced with H. neapolitanus Rubisco (HnRubisco) large and small subunit genes. We show that HnRubisco subunits can form functional L8S8 hexadecamers in tobacco chloroplasts at high efficiency, accounting for ∼40% of the wild-type tobacco Rubisco content. The chloroplast-expressed HnRubisco displayed a ∼2-fold greater carboxylation rate and supported a similar autotrophic growth rate of transgenic plants to that of wild-type in air supplemented with 1% CO2. This study represents a step toward the engineering of a fast and highly active Rubisco in chloroplasts to improve crop photosynthesis and growth.

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.

Physiological and Anatomical Responses of Faba Bean Plants Infected with Chocolate Spot Disease to Chemical Inducers

Plant diseases are biotic stresses that restrict crop plants' ability to develop and produce. Numerous foliar diseases, such as chocolate spots, can cause significant production losses in Vicia faba plants. Certain chemical inducers, including salicylic acid (SA), oxalic acid (OA), nicotinic acid (NA), and benzoic acid (BA), were used in this study to assess efficacy in controlling these diseases. A foliar spray of these phenolic acids was used to manage the impacts of the biotic stress resulting from disease incidence. All tested chemical inducers resulted in a significant decrease in disease severity. They also enhanced the defense system of treated plants through increasing antioxidant enzyme activity (Peroxidase, polyphenol oxidase, β-1, 3-glucanase, and chitinase) compared to the corresponding control. Healthy leaves of faba plants recorded the lowest (p < 0.05) values of all antioxidant activities compared to those plants infected by Botrytis fabae. Moreover, the separation of proteins using SDS-PAGE showed slight differences among treatments. Furthermore, foliar spray with natural organic acids reduced the adverse effects of fungal infection by expediting recovery. The SA (5 mM) treatment produced a pronounced increase in the upper, lower epidermis, palisade thickness, spongy tissues, midrib zone, length, and width of vascular bundle. The foliar application with other treatments resulted in a slight increase in the thickness of the examined layers, especially by benzoic acid. In general, all tested chemical inducers could alleviate the adverse effects of the biotic stress on faba bean plants infected by Botrytis fabae.

The stickers and spacers of Rubiscondensation: assembling the centrepiece of biophysical CO2-concentrating mechanisms

Aquatic autotrophs that fix carbon using ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) frequently expend metabolic energy to pump inorganic carbon towards the enzyme's active site. A central requirement of this strategy is the formation of highly concentrated Rubisco condensates (or Rubiscondensates) known as carboxysomes and pyrenoids, which have convergently evolved multiple times in prokaryotes and eukaryotes, respectively. Recent data indicate that these condensates form by the mechanism of liquid-liquid phase separation. This mechanism requires networks of weak multivalent interactions typically mediated by intrinsically disordered scaffold proteins. Here we comparatively review recent rapid developments that detail the determinants and precise interactions that underlie diverse Rubisco condensates. The burgeoning field of biomolecular condensates has few examples where liquid-liquid phase separation can be linked to clear phenotypic outcomes. When present, Rubisco condensates are essential for photosynthesis and growth, and they are thus emerging as powerful and tractable models to investigate the structure-function relationship of phase separation in biology.

The small subunit of Rubisco and its potential as an engineering target

Rubisco catalyses the first rate-limiting step in CO2 fixation and is responsible for the vast majority of organic carbon present in the biosphere. The function and regulation of Rubisco remain an important research topic and a longstanding engineering target to enhance the efficiency of photosynthesis for agriculture and green biotechnology. The most abundant form of Rubisco (Form I) consists of eight large and eight small subunits, and is found in all plants, algae, cyanobacteria, and most phototrophic and chemolithoautotrophic proteobacteria. Although the active sites of Rubisco are located on the large subunits, expression of the small subunit regulates the size of the Rubisco pool in plants and can influence the overall catalytic efficiency of the Rubisco complex. The small subunit is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. Here we review our current understanding of the role of the small subunit and our growing capacity to explore its potential to modulate Rubisco catalysis using engineering biology approaches.

Escherichia coli expressing chloroplast chaperones as a proxy to test heterologous Rubisco production in leaves

Rubisco is a fundamental enzyme in photosynthesis and therefore for life. Efforts to improve plant Rubisco performance have been hindered by the enzymes' complex chloroplast biogenesis requirements. New Synbio approaches, however, now allow the production of some plant Rubisco isoforms in Escherichia coli. While this enhances opportunities for catalytic improvement, there remain limitations in the utility of the expression system. Here we generate, optimize, and test a robust Golden Gate cloning E. coli expression system incorporating the protein folding machinery of tobacco chloroplasts. By comparing the expression of different plant Rubiscos in both E. coli and plastome-transformed tobacco, we show that the E. coli expression system can accurately predict high level Rubisco production in chloroplasts but poorly forecasts the biogenesis potential of isoforms with impaired production in planta. We reveal that heterologous Rubisco production in E. coli and tobacco plastids poorly correlates with Rubisco large subunit phylogeny. Our findings highlight the need to fully understand the factors governing Rubisco biogenesis if we are to deliver an efficient, low-cost screening tool that can accurately emulate chloroplast expression.

The discovery of rubisco

Rubisco is possibly the most important enzyme on Earth, certainly in terms of amount. This review describes the initial reports of ribulose 1,5-bisphosphate carboxylating activity. Discoveries of core concepts are described, including its quaternary structure, the requirement for post-translational modification, and its role as an oxygenase as well as a carboxylase. Finally, the requirement for numerous chaperonins for assembly of rubisco in plants is described.

Enhancing crop yields through improvements in the efficiency of photosynthesis and respiration

The rate with which crop yields per hectare increase each year is plateauing at the same time that human population growth and other factors increase food demand. Increasing yield potential (Y p ) of crops is vital to address these challenges. In this review, we explore a component ofY p that has yet to be optimised - that being improvements in the efficiency with which light energy is converted into biomass (ε c ) via modifications to CO2 fixed per unit quantum of light (α), efficiency of respiratory ATP production (ε prod ) and efficiency of ATP use (ε use ). For α, targets include changes in photoprotective machinery, ribulose bisphosphate carboxylase/oxygenase kinetics and photorespiratory pathways. There is also potential forε prod to be increased via targeted changes to the expression of the alternative oxidase and mitochondrial uncoupling pathways. Similarly, there are possibilities to improveε use via changes to the ATP costs of phloem loading, nutrient uptake, futile cycles and/or protein/membrane turnover. Recently developed high-throughput measurements of respiration can serve as a proxy for the cumulative energy cost of these processes. There are thus exciting opportunities to use our growing knowledge of factors influencing the efficiency of photosynthesis and respiration to create a step-change in yield potential of globally important crops.

Physiological and comparative transcriptome analysis of the response and adaptation mechanism of the photosynthetic function of mulberry (Morus alba L.) leaves to flooding stress

Flooding has become one of the major abiotic stresses that seriously affects plant growth and development owing to changes in the global precipitation pattern. Mulberry (Morus alba L.) is a desirable tree spePhysocarpus amurensis Maxim andcies with high ecological and economic benefits. To reveal the response and adaptive mechanisms of the photosynthetic functions of mulberry leaves to flooding stress, chlorophyll synthesis, photosynthetic electron transfer and the Calvin cycle were investigated by physiological studies combined with an analysis of the transcriptome. Flooding stress inhibited the synthesis of chlorophyll (Chl) and decreased its content in mulberry leaves. The sensitivity of Chl a to flooding stress was higher than that of Chl b owing to the changes of CHLG (LOC21385082) and CAO (LOC21408165) that encode genes during chlorophyll synthesis. The levels of expression of Chl b reductase NYC (LOC112094996) and NYC (LOC21385774), which are involved in Chl b degradation, were upregulated on the fifteenth day of flooding, which accelerated the transformation of Chl b to Chl a, and upregulated the expression of PPH (LOC21385040) and PAO (LOC21395013). This accelerated the degradation of chlorophyll. Flooding stress significantly inhibited the photosynthetic function of mulberry leaves. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes under different days of flooding stress indicated significant enrichment in Photosynthesis-antenna proteins (map00196), Photosynthesis (map00195) and Carbon fixation in photosynthetic organisms (map00710). On the fifth day of flooding, 7 and 5 genes that encode antenna proteins were identified on LHCII and LHCI, respectively. They were significantly downregulated, and the degree of downregulation increased as the trees were flooded longer. Therefore, the power of the leaves to capture solar energy and transfer this energy to the reaction center was reduced. The chlorophyll fluorescence parameters and related changes in the expression of genes in the transcriptome indicated that the PSII and PSI of mulberry leaves were damaged, and their activities decreased under flooding stress. On the fifth day of flooding, electron transfer on the PSII acceptor side of mulberry leaves was blocked, and the oxygen-evolving complex (OEC) on the donor side was damaged. On the tenth day of flooding, the thylakoid membranes of mulberry leaves were damaged. Five of the six coding genes that mapped to the OEC were significantly downregulated. Simultaneously, other coding genes located at the PSII reaction center and those located at the PSI reaction center, including Cytb6/f, PC, Fd, FNR and ATP, were also significantly downregulated. In addition, the gas exchange parameters (P_n, G_s, T_r, and C_i) of the leaves decreased after 10 days of flooding stress primarily owing to the stomatal factor. However, on the fifteenth day of flooding, the value for the intracellular concentration of CO₂ was significantly higher than that on the tenth day of flooding. In addition, the differentially expressed genes identified in the Calvin cycle were significantly downregulated, suggesting that in addition to stomatal factors, non-stomatal factors were also important factors that mediated the decrease in the photosynthetic capacity of mulberry leaves. In conclusion, the inhibition of growth of mulberry plants caused by flooding stress was primarily related to the inhibition of chlorophyll synthesis, antenna proteins, photosynthetic electron transfer and the Calvin cycle. The results of this study provide a theoretical basis for the response and mechanism of adaptation of the photosynthetic function of mulberry to flooding stress.

Designing epitope-focused vaccines via antigen reorientation

A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an "upside down" configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientation via oligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates.

GRAPHICAL ABSTRACT

Seasonal influenza vaccines induce a biased antibody response against the variable head of hemagglutinin, whereas conserved epitopes on the stem are a target for universal vaccines. Here we show that reorienting HA in an "upside-down" configuration sterically occludes the head and redirects the antibody response to the more exposed stem, thereby inducing broad cross-reactivity against hemagglutinins from diverse influenza strains.

Engineering Cupriavidus necator H16 for enhanced lithoautotrophic poly(3-hydroxybutyrate) production from CO2

Background

A representative hydrogen-oxidizing bacterium Cupriavidus necator H16 has attracted much attention as hosts to recycle carbon dioxide (CO₂) into a biodegradable polymer, poly(R)-3-hydroxybutyrate (PHB). Although C. necator H16 has been used as a model PHB producer, the PHB production rate from CO₂ is still too low for commercialization.

Results

Here, we engineer the carbon fixation metabolism to improve CO₂ utilization and increase PHB production. We explore the possibilities to enhance the lithoautotrophic cell growth and PHB production by introducing additional copies of transcriptional regulators involved in Calvin Benson Bassham (CBB) cycle. Both cbbR and regA-overexpressing strains showed the positive phenotypes for 11% increased biomass accumulation and 28% increased PHB production. The transcriptional changes of key genes involved in CO₂—fixing metabolism and PHB production were investigated.

Conclusions

The global transcriptional regulator RegA plays an important role in the regulation of carbon fixation and shows the possibility to improve autotrophic cell growth and PHB accumulation by increasing its expression level. This work represents another step forward in better understanding and improving the lithoautotrophic PHB production by C. necator H16.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01962-7.

Structural insights into cyanobacterial RuBisCO assembly coordinated by two chaperones Raf1 and RbcX

RuBisCO is the most abundant enzyme in nature, catalyzing the fixation of CO₂ in photosynthesis. Its common form consists of eight RbcL and eight RbcS subunits, the assembly of which requires a series of chaperones that include RbcX and RuBisCO accumulation factor 1 (Raf1). To understand how these RuBisCO-specific chaperones function during cyanobacterial RbcL₈RbcS₈ (L₈S₈) holoenzyme formation, we solved a 3.3-Å cryo-electron microscopy structure of a 32-subunit RbcL₈Raf1₈RbcX₁₆ (L₈F₈X₁₆) assembly intermediate from Anabaena sp. PCC 7120. Comparison to the previously resolved L₈F₈ and L₈X₁₆ structures together with biochemical assays revealed that the L₈F₈X₁₆ complex forms a rather dynamic structural intermediate, favoring RbcS displacement of Raf1 and RbcX. In vitro assays further demonstrated that both Raf1 and RbcX function to regulate RuBisCO condensate formation by restricting CcmM35 binding to the stably assembled L₈S₈ holoenzymes. Combined with previous findings, we propose a model on how Raf1 and RbcX work in concert to facilitate, and regulate, cyanobacterial RuBisCO assembly as well as disassembly of RuBisCO condensates.

Using synthetic biology to improve photosynthesis for sustainable food production

Photosynthesis is responsible for the primary productivity and maintenance of life on Earth, boosting biological activity and contributing to the maintenance of the environment. In the past, traditional crop improvement was considered sufficient to meet food demands, but the growing demand for food coupled with climate change has modified this scenario over the past decades. However, advances in this area have not focused on photosynthesis per se but rather on fixed carbon partitioning. In short, other approaches must be used to meet an increasing agricultural demand. Thus, several paths may be followed, from modifications in leaf shape and canopy architecture, improving metabolic pathways related to CO₂ fixation, the inclusion of metabolic mechanisms from other species, and improvements in energy uptake by plants. Given the recognized importance of photosynthesis, as the basis of the primary productivity on Earth, we here present an overview of the latest advances in attempts to improve plant photosynthetic performance. We focused on points considered key to the enhancement of photosynthesis, including leaf shape development, RuBisCO reengineering, Calvin-Benson cycle optimization, light use efficiency, the introduction of the C₄ cycle in C₃ plants and the inclusion of other CO₂ concentrating mechanisms (CCMs). We further provide compelling evidence that there is still room for further improvements. Finally, we conclude this review by presenting future perspectives and possible new directions on this subject.

Plants and water in a changing world: a physiological and ecological perspective

The reduction of greenhouse gases (GHGs) emission by replacing fossil energy stocks with carbon–neutral fuels is a major topic of the political and scientific debate on environmental sustainability. Such shift in energy sources is expected to curtail the accumulation rate of atmospheric CO₂, which is a strong infrared absorber and thus contributes to the global warming effect. Although such change would produce desirable outputs, the consequences of a drastic decrease in atmospheric CO₂ (the substrate of photosynthesis) should be carefully considered in the light of its potential impact on ecosystems stability and agricultural productivity. Indeed, plants regulate CO₂ uptake and water loss through the same anatomical structure: the leaf stomata. A reduced CO₂ availability is thus expected to enhance transpiration rate in plants decreasing their water use efficiency and imposing an increased water demand for both agricultural and wild ecosystems. We suggest that this largely underestimated issue should be duly considered when implementing policies that aim at the mitigation of global environmental changes and, at the same time, promote sustainable agricultural practices, include the preservation of biodiversity. Also, we underlie the important role(s) that modern biotechnology could play to tackle these global challenges by introducing new traits aimed at creating crop varieties with enhanced CO₂ capture and water- and light-use efficiency.

Review of the structures and functions of algal photoreceptors to optimize bioproduct production with novel bioreactor designs for strain improvement

Microalgae are important renewable feedstock to produce biodiesel and high-value chemicals. Different wavelengths of light influence the growth and metabolic activities of algae. Recent research has identified the light-sensing proteins called photoreceptors that respond to blue or red light. Structural elucidations of algal photoreceptors have gained momentum over recent years. These include channelrhodopsins, PHOT proteins, animal-like cryptochromes, blue-light sensors utilizing flavin-adenine dinucleotide (BLUF) proteins. Pulsing light has also been investigated as a means to optimize energy inputs into bioreactors. This review summarizes the current structural and functional basis of photoreceptor modulation to optimize the growth, production of carotenoids and other high-value metabolites from microalgae. The review also encompasses novel photobioreactor designs that implement different light regimes including light wavelengths and time to optimize algal growth and desired metabolite profiles for high-value products. This article is protected by copyright. All rights reserved.

Combinatorial use of environmental stresses and genetic engineering to increase ethanol titres in cyanobacteria

Current industrial bioethanol production by yeast through fermentation generates carbon dioxide. Carbon neutral bioethanol production by cyanobacteria uses biological fixation (photosynthesis) of carbon dioxide or other waste inorganic carbon sources, whilst being sustainable and renewable. The first ethanologenic cyanobacterial process was developed over two decades ago using Synechococcus elongatus PCC 7942, by incorporating the recombinant pdc and adh genes from Zymomonas mobilis. Further engineering has increased bioethanol titres 24-fold, yet current levels are far below what is required for industrial application. At the heart of the problem is that the rate of carbon fixation cannot be drastically accelerated and carbon partitioning towards bioethanol production impacts on cell fitness. Key progress has been achieved by increasing the precursor pyruvate levels intracellularly, upregulating synthetic genes and knocking out pathways competing for pyruvate. Studies have shown that cyanobacteria accumulate high proportions of carbon reserves that are mobilised under specific environmental stresses or through pathway engineering to increase ethanol production. When used in conjunction with specific genetic knockouts, they supply significantly more carbon for ethanol production. This review will discuss the progress in generating ethanologenic cyanobacteria through chassis engineering, and exploring the impact of environmental stresses on increasing carbon flux towards ethanol production.

The CbbQO-type rubisco activases encoded in carboxysome gene clusters can activate carboxysomal form IA rubiscos

The CO₂-fixing enzyme rubisco is responsible for almost all carbon fixation. This process frequently requires rubisco activase (Rca) machinery, which couples ATP hydrolysis to the removal of inhibitory sugar phosphates, including the rubisco substrate ribulose 1,5-bisphosphate (RuBP). Rubisco is sometimes compartmentalized in carboxysomes, bacterial microcompartments that enable a carbon dioxide concentrating mechanism (CCM). Characterized carboxysomal rubiscos, however, are not prone to inhibition, and often no activase machinery is associated with these enzymes. Here, we characterize two carboxysomal rubiscos of the form IA^C clade that are associated with CbbQO-type Rcas. These enzymes release RuBP at a much lower rate than the canonical carboxysomal rubisco from Synechococcus PCC6301. We found that CbbQO-type Rcas encoded in carboxysome gene clusters can remove RuBP and the tight-binding transition state analog carboxy-arabinitol 1,5-bisphosphate from cognate rubiscos. The Acidithiobacillus ferrooxidans genome encodes two form IA rubiscos associated with two sets of cbbQ and cbbO genes. We show that the two CbbQO activase systems display specificity for the rubisco enzyme encoded in the same gene cluster, and this property can be switched by substituting the C-terminal three residues of the large subunit. Our findings indicate that the kinetic and inhibitory properties of proteobacterial form IA rubiscos are diverse and predict that Rcas may be necessary for some α-carboxysomal CCMs. These findings will have implications for efforts aiming to introduce biophysical CCMs into plants and other hosts for improvement of carbon fixation of crops.

Amelioration of plant responses to drought under elevated CO2 by rejuvenating photosynthesis and nitrogen use efficiency: implications for future climate-resilient crops

The contemporary global agriculture is beset with serious threats from diverse eco-environmental conditions causing decreases in crop yields by ~ 15%. These yield losses might increase further due to climate change scenarios leading to increased food prices triggering social unrest and famines. Urbanization and industrialization are often associated with rapid increases in greenhouse gases (GHGs) especially atmospheric CO₂ concentration [(CO₂)]. Increase in atmospheric [CO₂] significantly improved crop photosynthesis and productivity initially which vary with plant species, genotype, [CO₂] exposure time and biotic as well as abiotic stress factors. Numerous attempts have been made using different plant species to unravel the physiological, cellular and molecular effects of elevated [CO₂] as well as drought. This review focuses on plant responses to elevated [CO₂] and drought individually as well as in combination with special reference to physiology of photosynthesis including its acclimation. Furthermore, the functional role of nitrogen use efficiency (NUE) and its relation to photosynthetic acclimation and crop productivity under elevated [CO₂] and drought are reviewed. In addition, we also discussed different strategies to ameliorate the limitations of ribulose-1,5-bisphosphate (RuBP) carboxylation and RuBP regeneration. Further, improved stomatal and mesophyll conductance and NUE for enhanced crop productivity under fast changing global climate conditions through biotechnological approaches are also discussed here. We conclude that multiple gene editing approaches for key events in photosynthetic processes would serve as the best strategy to generate resilient crop plants with improved productivity under fast changing climate.

Overexpression of Plasma Membrane H+-ATPase in Guard Cells Enhances Light-Induced Stomatal Opening, Photosynthesis, and Plant Growth in Hybrid Aspen

Stomata in the plant epidermis open in response to light and regulate CO₂ uptake for photosynthesis and transpiration for uptake of water and nutrients from roots. Light-induced stomatal opening is mediated by activation of the plasma membrane (PM) H⁺-ATPase in guard cells. Overexpression of PM H⁺-ATPase in guard cells promotes light-induced stomatal opening, enhancing photosynthesis and growth in Arabidopsis thaliana. In this study, transgenic hybrid aspens overexpressing Arabidopsis PM H⁺-ATPase (AHA2) in guard cells under the strong guard cell promoter Arabidopsis GC1 (AtGC1) showed enhanced light-induced stomatal opening, photosynthesis, and growth. First, we confirmed that AtGC1 induces GUS expression specifically in guard cells in hybrid aspens. Thus, we produced AtGC1::AHA2 transgenic hybrid aspens and confirmed expression of AHA2 in AtGC1::AHA2 transgenic plants. In addition, AtGC1::AHA2 transgenic plants showed a higher PM H⁺-ATPase protein level in guard cells. Analysis using a gas exchange system revealed that transpiration and the photosynthetic rate were significantly increased in AtGC1::AHA2 transgenic aspen plants. AtGC1::AHA2 transgenic plants showed a>20% higher stem elongation rate than the wild type (WT). Therefore, overexpression of PM H⁺-ATPase in guard cells promotes the growth of perennial woody plants.