Adjustments to Photosystem Stoichiometry and Electron Transfer Proteins Are Key to the Remarkably Fast Growth of the Cyanobacterium Synechococcus elongatus UTEX 2973

Chassis engineering for high light tolerance in microalgae and cyanobacteria

Oxygenic photosynthesis in microalgae and cyanobacteria is considered an important chassis to accelerate energy transition and mitigate global warming. Currently, cultivation systems for photosynthetic microbes for large-scale applications encountered excessive light exposure stress. High light stress can: affect photosynthetic efficiency, reduce productivity, limit cell growth, and even cause cell death. Deciphering photoprotection mechanisms and constructing high-light tolerant chassis have been recent research focuses. In this review, we first briefly introduce the self-protection mechanisms of common microalgae and cyanobacteria in response to high light stress. These mechanisms mainly include: avoiding excess light absorption, dissipating excess excitation energy, quenching excessive high-energy electrons, ROS detoxification, and PSII repair. We focus on the species-specific differences in these mechanisms as well as recent advancements. Then, we review engineering strategies for creating high-light tolerant chassis, such as: reducing the size of the light-harvesting antenna, optimizing non-photochemical quenching, optimizing photosynthetic electron transport, and enhancing PSII repair. Finally, we propose a comprehensive exploration of mechanisms: underlying identified high light tolerant chassis, identification of new genes pertinent to high light tolerance using innovative methodologies, harnessing CRISPR systems and artificial intelligence for chassis engineering modification, and introducing plant photoprotection mechanisms as future research directions.

Nutraceutical prospects of genetically engineered cyanobacteria- technological updates and significance

Genetically engineered cyanobacterial strains that have improved growth rate, biomass productivity, and metabolite productivity could be a better option for sustainable bio-metabolite production. The global demand for biobased metabolites with nutraceuticals and health benefits has increased due to their safety and plausible therapeutic and nutritional utility. Cyanobacteria are solar-powered green cellular factories that can be genetically tuned to produce metabolites with nutraceutical and pharmaceutical benefits. The present review discusses biotechnological endeavors for producing bioprospective compounds from genetically engineered cyanobacteria and discusses the challenges and troubleshooting faced during metabolite production. This review explores the cyanobacterial versatility, the use of engineered strains, and the techno-economic challenges associated with scaling up metabolite production from cyanobacteria. Challenges to produce cyanobacterial bioactive compounds with remarkable nutraceutical values have been discussed. Additionally, this review also summarises the challenges and future prospects of metabolite production from genetically engineered cyanobacteria as a sustainable approach.

Fast-growing cyanobacterial chassis for synthetic biology application

Carbon neutrality by 2050 has become one of the most urgent challenges the world faces today. To address the issue, it is necessary to develop and promote new technologies related with CO2 recycling. Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis, capable of fixing CO2 into biomass under sunlight and serving as one of the most important primary producers on earth. Notably, recent progress on synthetic biology has led to utilizing model cyanobacteria such as Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 as chassis for "light-driven autotrophic cell factories" to produce several dozens of biofuels and various fine chemicals directly from CO2. However, due to the slow growth rate and low biomass accumulation in the current chassis, the productivity for most products is still lower than the threshold necessary for large-scale commercial application, raising the importance of developing high-efficiency cyanobacterial chassis with fast growth and/or higher biomass accumulation capabilities. In this article, we critically reviewed recent progresses on identification, systems biology analysis, and engineering of fast-growing cyanobacterial chassis. Specifically, fast-growing cyanobacteria identified in recent years, such as S. elongatus UTEX 2973, S. elongatus PCC 11801, S. elongatus PCC 11802 and Synechococcus sp. PCC 11901 was comparatively analyzed. In addition, the progresses on their recent application in converting CO2 into chemicals, and genetic toolboxes developed for these new cyanobacterial chassis were discussed. Finally, the article provides insights into future challenges and perspectives on the synthetic biology application of cyanobacterial chassis.

Impact of irradiance and inorganic carbon availability on heterologous sucrose production in Synechococcus elongatus PCC 7942

Cyanobacteria have been proposed as a potential alternative carbohydrate feedstock and multiple species have been successfully engineered to secrete fermentable sugars. To date, the most productive cyanobacterial strains are those designed to secrete sucrose, yet there exist considerable differences in reported productivities across different model species and laboratories. In this study, we investigate how cultivation conditions (specifically, irradiance, CO2, and cultivator type) affect the productivity of sucrose-secreting Synechococcus elongatus PCC 7942. We find that S. elongatus produces the highest sucrose yield in irradiances far greater than what is often experimentally utilized, and that high light intensities are tolerated by S. elongatus, especially under higher density cultivation where turbidity may attenuate the effective light experienced in the culture. By increasing light and inorganic carbon availability, S. elongatus cscB/sps produced a total of 3.8 g L-1 of sucrose and the highest productivity within that period being 47.8 mg L-1 h-1. This study provides quantitative description of the impact of culture conditions on cyanobacteria-derived sucrose that may assist to standardize cross-laboratory comparisons and demonstrates a significant capacity to improve productivity via optimizing cultivation conditions.

UV-A radiation increases biomass yield by enhancing energy flow and carbon assimilation in the edible cyanobacterium Nostoc sphaeroides

Ultraviolet (UV) A radiation (315-400 nm) is the predominant component of solar UV radiation that reaches the Earth's surface. However, the underlying mechanisms of the positive effects of UV-A on photosynthetic organisms have not yet been elucidated. In this study, we investigated the effects of UV-A radiation on the growth, photosynthetic ability, and metabolome of the edible cyanobacterium Nostoc sphaeroides. Exposures to 5-15 W m-2 (15-46 µmol photons m-2 s-1) UV-A and 4.35 W m-2 (20 μmol photons m-2 s-1) visible light for 16 days significantly increased the growth rate and biomass production of N. sphaeroides cells by 18%-30% and 15%-56%, respectively, compared to the non-UV-A-acclimated cells. Additionally, the UV-A-acclimated cells exhibited a 1.8-fold increase in the cellular nicotinamide adenine dinucleotide phosphate (NADP) pool with an increase in photosynthetic capacity (58%), photosynthetic efficiency (24%), QA re-oxidation, photosystem I abundance, and cyclic electron flow (87%), which further led to an increase in light-induced NADPH generation (31%) and ATP content (83%). Moreover, the UV-A-acclimated cells showed a 2.3-fold increase in ribulose-1,5-bisphosphate carboxylase/oxygenase activity, indicating an increase in their carbon-fixing capacity. Gas chromatography-mass spectrometry-based metabolomics further revealed that UV-A radiation upregulated the energy-storing carbon metabolism, as evidenced by the enhanced accumulation of sugars, fatty acids, and citrate in the UV-A-acclimated cells. Therefore, our results demonstrate that UV-A radiation enhances energy flow and carbon assimilation in the cyanobacterium N. sphaeroides.IMPORTANCEUltraviolet (UV) radiation exerts harmful effects on photo-autotrophs; however, several studies demonstrated the positive effects of UV radiation, especially UV-A radiation (315-400 nm), on primary productivity. Therefore, understanding the underlying mechanisms associated with the promotive effects of UV-A radiation on primary productivity can facilitate the application of UV-A for CO2 sequestration and lead to the advancement of photobiological sciences. In this study, we used the cyanobacterium Nostoc sphaeroides, which has an over 1,700-year history of human use as food and medicine, to explore its photosynthetic acclimation response to UV-A radiation. As per our knowledge, this is the first study to demonstrate that UV-A radiation increases the biomass yield of N. sphaeroides by enhancing energy flow and carbon assimilation. Our findings provide novel insights into UV-A-mediated photosynthetic acclimation and provide a scientific basis for the application of UV-A radiation for optimizing light absorption capacity and enhancing CO2 sequestration in the frame of a future CO2 neutral, circular, and sustainable bioeconomy.

Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

Cyanobacteria are photosynthetic organisms that have garnered significant recognition as potential hosts for sustainable bioproduction. However, their complex regulatory networks pose significant challenges to major metabolic engineering efforts, thereby limiting their feasibility as production hosts. Genome streamlining has been demonstrated to be a successful approach for improving productivity and fitness in heterotrophs but is yet to be explored to its full potential in phototrophs. Here, we present the systematic reduction of the genome of the cyanobacterium exhibiting the fastest exponential growth, Synechococcus elongatus UTEX 2973. This work, the first of its kind in a photoautotroph, involved an iterative process using state-of-the-art genome-editing technology guided by experimental analysis and computational tools. CRISPR-Cas3 enabled large, progressive deletions of predicted dispensable regions and aided in the identification of essential genes. The large deletions were combined to obtain a strain with 55-kb genome reduction. The strains with streamlined genome showed improvement in growth (up to 23%) and productivity (by 22.7%) as compared to the wild type (WT). This streamlining strategy not only has the potential to develop cyanobacterial strains with improved growth and productivity traits but can also facilitate a better understanding of their genome-to-phenome relationships.IMPORTANCEGenome streamlining is an evolutionary strategy used by natural living systems to dispense unnecessary genes from their genome as a mechanism to adapt and evolve. While this strategy has been successfully borrowed to develop synthetic heterotrophic microbial systems with desired phenotype, it has not been extensively explored in photoautotrophs. Genome streamlining strategy incorporates both computational predictions to identify the dispensable regions and experimental validation using genome-editing tool, and in this study, we have employed a modified strategy with the goal to minimize the genome size to an extent that allows optimal cellular fitness under specified conditions. Our strategy has explored a novel genome-editing tool in photoautotrophs, which, unlike other existing tools, enables large, spontaneous optimal deletions from the genome. Our findings demonstrate the effectiveness of this modified strategy in obtaining strains with streamlined genome, exhibiting improved fitness and productivity.

Machine learning predicts system-wide metabolic flux control in cyanobacteria

Metabolic fluxes and their control mechanisms are fundamental in cellular metabolism, offering insights for the study of biological systems and biotechnological applications. However, quantitative and predictive understanding of controlling biochemical reactions in microbial cell factories, especially at the system level, is limited. In this work, we present ARCTICA, a computational framework that integrates constraint-based modelling with machine learning tools to address this challenge. Using the model cyanobacterium Synechocystis sp. PCC 6803 as chassis, we demonstrate that ARCTICA effectively simulates global-scale metabolic flux control. Key findings are that (i) the photosynthetic bioproduction is mainly governed by enzymes within the Calvin-Benson-Bassham (CBB) cycle, rather than by those involve in the biosynthesis of the end-product, (ii) the catalytic capacity of the CBB cycle limits the photosynthetic activity and downstream pathways and (iii) ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a major, but not the most, limiting step within the CBB cycle. Predicted metabolic reactions qualitatively align with prior experimental observations, validating our modelling approach. ARCTICA serves as a valuable pipeline for understanding cellular physiology and predicting rate-limiting steps in genome-scale metabolic networks, and thus provides guidance for bioengineering of cyanobacteria.

Advances in light system engineering across the phototrophic spectrum

Current work in photosynthetic engineering is progressing along the lines of cyanobacterial, microalgal, and plant research. These are interconnected through the fundamental mechanisms of photosynthesis and advances in one field can often be leveraged to improve another. It is worthwhile for researchers specializing in one or more of these systems to be aware of the work being done across the entire research space as parallel advances of techniques and experimental approaches can often be applied across the field of photosynthesis research. This review focuses on research published in recent years related to the light reactions of photosynthesis in cyanobacteria, eukaryotic algae, and plants. Highlighted are attempts to improve photosynthetic efficiency, and subsequent biomass production. Also discussed are studies on cross-field heterologous expression, and related work on augmented and novel light capture systems. This is reviewed in the context of translatability in research across diverse photosynthetic organisms.

Cost-effective production of bioplastic polyhydroxybutyrate via introducing heterogeneous constitutive promoter and elevating acetyl-Coenzyme A pool of rapidly growing cyanobacteria

Bioplastic production using cyanobacteria can be an effective strategy to cope with environmental problems caused by using petroleum-based plastics. Synechococcus elongatus UTEX 2973 with heterogeneous phaCAB can produce bioplastic polyhydroxybutyrate (PHB) with a high CO2 uptake rate. For cost-effective production of PHB in S. elongatus UTEX 2973, phaCAB was expressed by the constitutive Pcpc560, resulting in the production of 226 mg/L of PHB by only photoautotrophic cultivation without the addition of inducer. Several culture conditions were applied to increase PHB productivity, and when acetate was supplied at a concentration of 1 g/L as an organic carbon source, productivity significantly increased resulting in 607.2 mg/L of PHB and additive cost reduction of more than 300 times was achieved compared to IPTG. Consequently, these results suggest the possibility of cyanobacteria as an agent that can economically produce PHB and as a solution to the problem of petroleum-based plastics.

Genomic imprints of unparalleled growth

Chlorella ohadii was isolated from desert biological soil crusts, one of the harshest habitats on Earth, and is emerging as an exciting new green model for studying growth, photosynthesis and metabolism under a wide range of conditions. Here, we compared the genome of C. ohadii, the fastest growing alga on record, to that of other green algae, to reveal the genomic imprints empowering its unparalleled growth rate and resistance to various stressors, including extreme illumination. This included the genome of its close relative, but slower growing and photodamage sensitive, C. sorokiniana UTEX 1663. A larger number of ribosome-encoding genes, high intron abundance, increased codon bias and unique genes potentially involved in metabolic flexibility and resistance to photodamage are all consistent with the faster growth of C. ohadii. Some of these characteristics highlight general trends in Chlorophyta and Chlorella spp. evolution, and others open new broad avenues for mechanistic exploration of their relationship with growth. This work entails a unique case study for the genomic adaptations and costs of exceptionally fast growth and sheds light on the genomic signatures of fast growth in photosynthetic cells. It also provides an important resource for future studies leveraging the unique properties of C. ohadii for photosynthesis and stress response research alongside their utilization for synthetic biology and biotechnology aims.

Molecular Bulkiness of a Single Amino Acid in the F1 α-Subunit Determines the Robustness of Cyanobacterial ATP Synthase

Cyanobacteria are promising photosynthetic organisms owing to their ease of genetic manipulation. Among them, Synechococcus elongatus UTEX 2973 exhibits faster growth, higher biomass production efficiency and more robust stress tolerance compared with S. elongatus PCC 7942. This is due to specific genetic differences, including four single-nucleotide polymorphisms (SNPs) in three genes. One of these SNPs alters an amino acid at position 252 of the FoF1 ATP synthase α-subunit from Tyr to Cys (αY252C) in S. elongatus 7942. This change has been shown to significantly affect growth rate and stress tolerance, specifically in S. elongatus. Furthermore, experimental substitutions with several other amino acids have been shown to alter the ATP synthesis rate in the cell. In the present study, we introduced identical amino acid substitutions into Synechocystis sp. PCC 6803 at position 252 to elucidate the amino acid's significance and generality across cyanobacteria. We investigated the resulting impact on growth, intracellular enzyme complex levels, intracellular ATP levels and enzyme activity. The results showed that the αY252C substitution decreased growth rate and high-light tolerance. This indicates that a specific bulkiness of this amino acid's side chain is important for maintaining cell growth. Additionally, a remarkable decrease in the membrane-bound enzyme complex level was observed. However, the αY252C substitution did not affect enzyme activity or intracellular ATP levels. Although the mechanism of growth suppression remains unknown, the amino acid at position 252 is expected to play an important role in enzyme complex formation.

Cell surface composition, released polysaccharides, and ionic strength mediate fast sedimentation in the cyanobacterium Synechococcus elongatus PCC 7942

Cyanobacteria are photosynthetic prokaryotes of high ecological and biotechnological relevance that have been cultivated in laboratories around the world for more than 70 years. Prolonged laboratory culturing has led to multiple microevolutionary events and the appearance of a large number of 'domesticated' substrains among model cyanobacteria. Despite its widespread occurrence, strain domestication is still largely ignored. In this work we describe Synechococcus elongatus PCC 7942-KU, a novel domesticated substrain of the model cyanobacterium S. elongatus PCC 7942, which presents a fast-sedimenting phenotype. Under higher ionic strengths the sedimentation rate increased leading to complete sedimentation in just 12 h. Through whole genome sequencing and gene deletion, we demonstrated that the Group 3 alternative sigma factor F plays a key role in cell sedimentation. Further analysis showed that significant changes in cell surface structures and a three-fold increase in released polysaccharides lead to the appearance of a fast-sedimenting phenotype. This work sheds light on the determinants of the planktonic to benthic transitions and provides genetic targets to generate fast-sedimenting strains that could unlock cost-effective cyanobacterial harvesting at scale.

Antenna Modification in a Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973 Leads to Improved Efficiency and Carbon-Neutral Productivity

Our planet is sustained by sunlight, the primary energy source made accessible to all life forms by photoautotrophs. Photoautotrophs are equipped with light-harvesting complexes (LHCs) that enable efficient capture of solar energy, particularly when light is limiting. However, under high light, LHCs can harvest photons in excess of the utilization capacity of cells, causing photodamage. This damaging effect is most evident when there is a disparity between the amount of light harvested and carbon available. Cells strive to circumvent this problem by dynamically adjusting the antenna structure in response to the changing light signals, a process known to be energetically expensive. Much emphasis has been laid on elucidating the relationship between antenna size and photosynthetic efficiency and identifying strategies to synthetically modify antennae for optimal light capture. Our study is an effort in this direction and investigates the possibility of modifying phycobilisomes, the LHCs present in cyanobacteria, the simplest of photoautotrophs. We systematically truncate the phycobilisomes of Synechococcus elongatus UTEX 2973, a widely studied, fast-growing model cyanobacterium and demonstrate that partial truncation of its antenna can lead to a growth advantage of up to 36% compared to the wild type and an increase in sucrose titer of up to 22%. In contrast, targeted deletion of the linker protein which connects the first phycocyanin rod to the core proved detrimental, indicating that the core alone is not enough, and it is essential to maintain a minimal rod-core structure for efficient light harvest and strain fitness. IMPORTANCE Light energy is essential for the existence of life on this planet, and only photosynthetic organisms, equipped with light-harvesting antenna protein complexes, can capture this energy, making it readily accessible to all other life forms. However, these light-harvesting antennae are not designed to function optimally under extreme high light, a condition which can cause photodamage and significantly reduce photosynthetic productivity. In this study, we attempt to assess the optimal antenna structure for a fast-growing, high-light tolerant photosynthetic microbe with the goal of improving its productivity. Our findings provide concrete evidence that although the antenna complex is essential, antenna modification is a viable strategy to maximize strain performance under controlled growth conditions. This understanding can also be translated into identifying avenues to improve light harvesting efficiency in higher photoautotrophs.

Solar-powered P450 catalysis: Engineering electron transfer pathways from photosynthesis to P450s

With the increasing focus on green chemistry, biocatalysis is becoming more widely used in the pharmaceutical and other chemical industries for sustainable production of high value and structurally complex chemicals. Cytochrome P450 monooxygenases (P450s) are attractive biocatalysts for industrial application due to their ability to transform a huge range of substrates in a stereo- and regiospecific manner. However, despite their appeal, the industrial application of P450s is limited by their dependence on costly reduced nicotinamide adenine dinucleotide phosphate (NADPH) and one or more auxiliary redox partner proteins. Coupling P450s to the photosynthetic machinery of a plant allows photosynthetically-generated electrons to be used to drive catalysis, overcoming this cofactor dependency. Thus, photosynthetic organisms could serve as photobioreactors with the capability to produce value-added chemicals using only light, water, CO2 and an appropriate chemical as substrate for the reaction/s of choice, yielding new opportunities for producing commodity and high-value chemicals in a carbon-negative and sustainable manner. This review will discuss recent progress in using photosynthesis for light-driven P450 biocatalysis and explore the potential for further development of such systems.

Changes in intracellular energetic and metabolite states due to increased galactolipid levels in Synechococcus elongatus PCC 7942

The lipid composition of thylakoid membranes is conserved from cyanobacteria to green plants. However, the biosynthetic pathways of galactolipids, the major components of thylakoid membranes, are known to differ substantially between cyanobacteria and green plants. We previously reported on a transformant of the unicellular rod-shaped cyanobacterium Synechococcus elongatus PCC 7942, namely SeGPT, in which the synthesis pathways of the galactolipids monogalactosyldiacylglycerol and digalactosyldiacylglycerol are completely replaced by those of green plants. SeGPT exhibited increased galactolipid content and could grow photoautotrophically, but its growth rate was slower than that of wild-type S. elongatus PCC 7942. In the present study, we investigated pleiotropic effects that occur in SeGPT and determined how its increased lipid content affects cell proliferation. Microscopic observations revealed that cell division and thylakoid membrane development are impaired in SeGPT. Furthermore, physiological analyses indicated that the bioenergetic state of SeGPT is altered toward energy storage, as indicated by increased levels of intracellular ATP and glycogen. We hereby report that we have identified a new promising candidate as a platform for material production by modifying the lipid synthesis system in this way.

Cyanobacterial Bioenergetics in Relation to Cellular Growth and Productivity

Cyanobacteria, the evolutionary originators of oxygenic photosynthesis, have the capability to convert CO2, water, and minerals into biomass using solar energy. This process is driven by intricate bioenergetic mechanisms that consist of interconnected photosynthetic and respiratory electron transport chains coupled. Over the last few decades, advances in physiochemical analysis, molecular genetics, and structural analysis have enabled us to gain a more comprehensive understanding of cyanobacterial bioenergetics. This includes the molecular understanding of the primary energy conversion mechanisms as well as photoprotective and other dissipative mechanisms that prevent photodamage when the rates of photosynthetic output, primarily in the form of ATP and NADPH, exceed the rates that cellular assimilatory processes consume these photosynthetic outputs. Despite this progress, there is still much to learn about the systems integration and the regulatory circuits that control expression levels for optimal cellular abundance and activity of the photosynthetic complexes and the cellular components that convert their products into biomass. With an improved understanding of these regulatory principles and mechanisms, it should be possible to optimally modify cyanobacteria for enhanced biotechnological purposes.

Genomic analysis and biochemical profiling of an unaxenic strain of Synechococcus sp. isolated from the Peruvian Amazon Basin region

Cyanobacteria are diverse photosynthetic microorganisms able to produce a myriad of bioactive chemicals. To make possible the rational exploitation of these microorganisms, it is fundamental to know their metabolic capabilities and to have genomic resources. In this context, the main objective of this research was to determine the genome features and the biochemical profile of Synechococcus sp. UCP002. The cyanobacterium was isolated from the Peruvian Amazon Basin region and cultured in BG-11 medium. Growth parameters, genome features, and the biochemical profile of the cyanobacterium were determined using standardized methods. Synechococcus sp. UCP002 had a specific growth rate of 0.086 ± 0.008 μ and a doubling time of 8.08 ± 0.78 h. The complete genome of Synechococcus sp. UCP002 had a size of ∼3.53 Mb with a high coverage (∼200x), and its quality parameters were acceptable (completeness = 99.29%, complete and single-copy genes = 97.5%, and contamination = 0.35%). Additionally, the cyanobacterium had six plasmids ranging from 24 to 200 kbp. The annotated genome revealed ∼3,422 genes, ∼ 3,374 protein-coding genes (with ∼41.31% hypothetical protein-coding genes), two CRISPR Cas systems, and 61 non-coding RNAs. Both the genome and plasmids had the genes for prokaryotic defense systems. Additionally, the genome had genes coding the transcription factors of the metalloregulator ArsR/SmtB family, involved in sensing heavy metal pollution. The biochemical profile showed primary nutrients, essential amino acids, some essential fatty acids, pigments (e.g., all-trans-β-carotene, chlorophyll a, and phycocyanin), and phenolic compounds. In conclusion, Synechococcus sp. UCP002 shows biotechnological potential to produce human and animal nutrients and raw materials for biofuels and could be a new source of genes for synthetic biological applications.

Native architecture and acclimation of photosynthetic membranes in a fast-growing cyanobacterium

Efficient solar energy conversion is ensured by the organization, physical association, and physiological coordination of various protein complexes in photosynthetic membranes. Here, we visualize the native architecture and interactions of photosynthetic complexes within the thylakoid membranes from a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) using high-resolution atomic force microscopy. In the Syn2973 thylakoid membranes, both photosystem I (PSI)-enriched domains and crystalline photosystem II (PSII) dimer arrays were observed, providing favorable membrane environments for photosynthetic electron transport. The high light (HL)-adapted thylakoid membranes accommodated a large amount of PSI complexes, without the incorporation of iron-stress-induced protein A (IsiA) assemblies and formation of IsiA-PSI supercomplexes. In the iron deficiency (Fe-)-treated thylakoid membranes, in contrast, IsiA proteins densely associated with PSI, forming the IsiA-PSI supercomplexes with varying assembly structures. Moreover, type-I NADH dehydrogenase-like complexes (NDH-1) were upregulated under the HL and Fe- conditions and established close association with PSI complexes to facilitate cyclic electron transport. Our study provides insight into the structural heterogeneity and plasticity of the photosynthetic apparatus in the context of their native membranes in Syn2973 under environmental stress. Advanced understanding of the photosynthetic membrane organization and adaptation will provide a framework for uncovering the molecular mechanisms of efficient light harvesting and energy conversion.

A droplet-based microfluidic platform enables high-throughput combinatorial optimization of cyanobacterial cultivation

Cyanobacteria are fast-growing, genetically accessible, photoautotrophs. Therefore, they have attracted interest as sustainable production platforms. However, the lack of techniques to systematically optimize cultivation parameters in a high-throughput manner is holding back progress towards industrialization. To overcome this bottleneck, here we introduce a droplet-based microfluidic platform capable of one- (1D) and two-dimension (2D) screening of key parameters in cyanobacterial cultivation. We successfully grew three different unicellular, biotechnologically relevant, cyanobacteria: Synechocystis sp. PCC 6803, Synechococcus elongatus UTEX 2973 and Synechococcus sp. UTEX 3154. This was followed by a highly-resolved 1D screening of nitrate, phosphate, carbonate, and salt concentrations. The 1D screening results suggested that nitrate and/or phosphate may be limiting nutrients in standard cultivation media. Finally, we use 2D screening to determine the optimal N:P ratio of BG-11. Application of the improved medium composition in a high-density cultivation setup led to an increase in biomass yield of up to 15.7%. This study demonstrates that droplet-based microfluidics can decrease the volume required for cyanobacterial cultivation and screening up to a thousand times while significantly increasing the multiplexing capacity. Going forward, microfluidics have the potential to play a significant role in the industrial exploitation of cyanobacteria.

Engineering plant family TPS into cyanobacterial host for terpenoids production

Terpenoids are synthesized naturally by plants as secondary metabolites, and are diverse and complex in structure with multiple applications in bioenergy, food, cosmetics, and medicine. This makes the production of terpenoids such as isoprene, β-phellandrene, farnesene, amorphadiene, and squalene valuable, owing to which their industrial demand cannot be fulfilled exclusively by plant sources. They are synthesized via the Methylerythritol phosphate pathway (MEP) and the Mevalonate pathway (MVA), both existing in plants. The advent of genetic engineering and the latest accomplishments in synthetic biology and metabolic engineering allow microbial synthesis of terpenoids. Cyanobacteria manifest to be the promising hosts for this, utilizing sunlight and CO₂. Cyanobacteria possess MEP pathway to generate precursors for terpenoid synthesis. The terpenoid synthesis can be amplified by overexpressing the MEP pathway and engineering MVA pathway genes. According to the desired terpenoid, terpene synthases unique to the plant kingdom must be incorporated in cyanobacteria. Engineering an organism to be used as a cell factory comes with drawbacks such as hampered cell growth and disturbance in metabolic flux. This review set forth a comparison between MEP and MVA pathways, strategies to overexpress these pathways with their challenges.

A Ubiquitously Conserved Cyanobacterial Protein Phosphatase Essential for High Light Tolerance in a Fast-Growing Cyanobacterium

Synechococcus elongatus UTEX 2973, the fastest-growing cyanobacterial strain known, optimally grows under extreme high light (HL) intensities of 1,500-2,500 μmol photons m^-2 s^-1, which is lethal to most other photosynthetic microbes. We leveraged the few genetic differences between Synechococcus 2973 and the HL sensitive strain Synechococcus elongatus PCC 7942 to unravel factors essential for the high light tolerance. We identified a novel protein in Synechococcus 2973 that we have termed HltA for High light tolerance protein A. Using bioinformatic tools, we determined that HltA contains a functional PP2C-type protein phosphatase domain. Phylogenetic analysis showed that the PP2C domain belongs to the bacterial-specific Group II family and is closely related to the environmental stress response phosphatase RsbU. Additionally, we showed that unlike any previously described phosphatases, HltA contains a single N-terminal regulatory GAF domain. We found hltA to be ubiquitous throughout cyanobacteria, indicative of its potentially important role in the photosynthetic lifestyle of these oxygenic phototrophs. Mutations in the hltA gene resulted in severe defects specific to high light growth. These results provide evidence that hltA is a key factor in the tolerance of Synechococcus 2973 to high light and will open new insights into the mechanisms of cyanobacterial light stress response. IMPORTANCE Cyanobacteria are a diverse group of photosynthetic prokaryotes. The cyanobacterium Synechococcus 2973 is a high light tolerant strain with industrial promise due to its fast growth under high light conditions and the availability of genetic modification tools. Currently, little is known about the high light tolerance mechanisms of Synechococcus 2973, and there are many unknowns overall regarding high light tolerance of cyanobacteria. In this study, a comparative genomic analysis of Synechococcus 2973 identified a single nucleotide polymorphism in a locus encoding a serine phosphatase as a key factor for high light tolerance. This novel GAF-containing phosphatase was found to be the sole Group II metal-dependent protein phosphatase that is evolutionarily conserved throughout cyanobacteria. These results shed new light on the light response mechanisms of Synechococcus 2973, improving our understanding of environmental stress response. Additionally, this work will help facilitate the development of Synechococcus 2973 as an industrially useful organism.

Exploring cyanobacterial diversity for sustainable biotechnology

Cyanobacteria are an evolutionarily ancient and diverse group of microorganisms. Their genetic diversity has 
allowed them to occupy and play vital roles in a wide range of ecological niches, from desert soil crusts to tropical oceans. Owing to bioprospecting efforts and the development of new platform technologies enabling their study and manipulation, our knowledge of cyanobacterial metabolism is rapidly expanding. This review explores our current understanding of the genetic and metabolic features of cyanobacteria, from the more established cyanobacterial model strains to the newly isolated/described species, particularly the fast-growing, highly productive, and genetically amenable strains, as promising chassis for renewable biotechnology. It also discusses emerging technologies for their study and manipulation, enabling researchers to harness the astounding diversity of the cyanobacterial genomic and metabolic treasure trove towards the establishment of a sustainable bioeconomy.

Exploitation of Hetero- and Phototrophic Metabolic Modules for Redox-Intensive Whole-Cell Biocatalysis

The successful realization of a sustainable manufacturing bioprocess and the maximization of its production potential and capacity are the main concerns of a bioprocess engineer. A main step towards this endeavor is the development of an efficient biocatalyst. Isolated enzyme(s), microbial cells, or (immobilized) formulations thereof can serve as biocatalysts. Living cells feature, beside active enzymes, metabolic modules that can be exploited to support energy-dependent and multi-step enzyme-catalyzed reactions. Metabolism can sustainably supply necessary cofactors or cosubstrates at the expense of readily available and cheap resources, rendering external addition of costly cosubstrates unnecessary. However, for the development of an efficient whole-cell biocatalyst, in depth comprehension of metabolic modules and their interconnection with cell growth, maintenance, and product formation is indispensable. In order to maximize the flux through biosynthetic reactions and pathways to an industrially relevant product and respective key performance indices (i.e., titer, yield, and productivity), existing metabolic modules can be redesigned and/or novel artificial ones established. This review focuses on whole-cell bioconversions that are coupled to heterotrophic or phototrophic metabolism and discusses metabolic engineering efforts aiming at 1) increasing regeneration and supply of redox equivalents, such as NAD(P/H), 2) blocking competing fluxes, and 3) increasing the availability of metabolites serving as (co)substrates of desired biosynthetic routes.

Synthetic Biology Approaches for Improving Chemical Production in Cyanobacteria

Biological chemical production has gained traction in recent years as a promising renewable alternative to traditional petrochemical based synthesis. Of particular interest in the field of metabolic engineering are photosynthetic microorganisms capable of sequestering atmospheric carbon dioxide. CO₂ levels have continued to rise at alarming rates leading to an increasingly uncertain climate. CO₂ can be sequestered by engineered photosynthetic microorganisms and used for chemical production, representing a renewable production method for valuable chemical commodities such as biofuels, plastics, and food additives. The main challenges in using photosynthetic microorganisms for chemical production stem from the seemingly inherent limitations of carbon fixation and photosynthesis resulting in slower growth and lower average product titers compared to heterotrophic organisms. Recently, there has been an increase in research around improving photosynthetic microorganisms as renewable chemical production hosts. This review will discuss the various efforts to overcome the intrinsic inefficiencies of carbon fixation and photosynthesis, including rewiring carbon fixation and photosynthesis, investigating alternative carbon fixation pathways, installing sugar catabolism to supplement carbon fixation, investigating newly discovered fast growing photosynthetic species, and using new synthetic biology tools such as CRISPR to radically alter metabolism.

Electrochemically Driven Photosynthetic Electron Transport in Cyanobacteria Lacking Photosystem II

Light-activated photosystem II (PSII) carries out the critical step of splitting water in photosynthesis. However, PSII is susceptible to light-induced damage. Here, results are presented from a novel microbial electro-photosynthetic system (MEPS) that uses redox mediators in conjunction with an electrode to drive electron transport in live Synechocystis (ΔpsbB) cells lacking PSII. MEPS-generated, light-dependent current increased with light intensity up to 2050 μmol photons m^-2 s^-1, which yielded a delivery rate of 113 μmol electrons h^-1 mg-chl^-1 and an average current density of 150 A m^-2 s^-1 mg-chl^-1. P700⁺ re-reduction kinetics demonstrated that initial rates exceeded wildtype PSII-driven electron delivery. The electron delivery occurs ahead of the cytochrome b₆f complex to enable both NADPH and ATP production. This work demonstrates an electrochemical system that can drive photosynthetic electron transport, provides a platform for photosynthetic foundational studies, and has the potential for improving photosynthetic performance at high light intensities.

Machine learning-informed and synthetic biology-enabled semi-continuous algal cultivation to unleash renewable fuel productivity

Algal biofuel is regarded as one of the ultimate solutions for renewable energy, but its commercialization is hindered by growth limitations caused by mutual shading and high harvest costs. We overcome these challenges by advancing machine learning to inform the design of a semi-continuous algal cultivation (SAC) to sustain optimal cell growth and minimize mutual shading. An aggregation-based sedimentation (ABS) strategy is then designed to achieve low-cost biomass harvesting and economical SAC. The ABS is achieved by engineering a fast-growing strain, Synechococcus elongatus UTEX 2973, to produce limonene, which increases cyanobacterial cell surface hydrophobicity and enables efficient cell aggregation and sedimentation. SAC unleashes cyanobacterial growth potential with 0.1 g/L/hour biomass productivity and 0.2 mg/L/hour limonene productivity over a sustained period in photobioreactors. Scaling-up the SAC with an outdoor pond system achieves a biomass yield of 43.3 g/m²/day, bringing the minimum biomass selling price down to approximately $281 per ton.

Growth limitation caused by mutual shading and the high harvest cost hamper algal biofuel production. Here, the authors overcome these two problems by designing a semi-continuous algal cultivation system and an aggregation-based sedimentation strategy to achieve high levels production of biomass and limonene.

Engineering Natural Competence into the Fast-Growing Cyanobacterium Synechococcus elongatus Strain UTEX 2973

Natural transformation is the process by which bacteria actively take up and integrate extracellular DNA into their genomes. In cyanobacteria, natural transformation has only been experimentally demonstrated in a few species. Although cyanobacteria are important model systems for studying photosynthesis and circadian cycling, natural transformation in cyanobacteria has not been characterized to the degree that the process has been studied in other Gram-negative bacteria. Two cyanobacterial species that are 99.8% genetically identical provide a unique opportunity to better understand the nuances of natural transformation in cyanobacteria: Synechococcus elongatus PCC 7942 and Synechococcus elongatus UTEX 2973 (hereafter called Synechococcus 7942 and Synechococcus 2973, respectively). Synechococcus 7942 is a naturally transformable model system, while Synechococcus 2973 is a recently discovered species that is not naturally competent. Taking only 1.5 h to replicate, Synechococcus 2973 is the fastest-growing cyanobacterial species known and thus is a strong candidate for serving as a model organism. However, its inability to undergo natural transformation has prevented it from becoming a widely used model system. By substituting polymorphic alleles from Synechococcus 7942 for native Synechococcus 2973 alleles, natural transformation was introduced into Synechococcus 2973. Two genetic loci were found to be involved in differential natural competence between the two organisms: transformation pilus component pilN and circadian transcriptional master regulator rpaA. By using targeted genome editing and enrichment outgrowth, a strain that was both naturally transformable and fast-growing was created. This new Synechococcus 2973-T strain will serve as a valuable resource to the cyanobacterial research community. IMPORTANCE Certain bacterial species have the ability to take up naked extracellular DNA and integrate it into their genomes. This process is known as natural transformation and is widely considered to play a major role in bacterial evolution. Because of the ease of introducing new genes into naturally transformable organisms, this capacity is also highly valued in the laboratory. Cyanobacteria are photosynthetic and can therefore serve as model systems for some important aspects of plant physiology. Here, we describe the creation of a modified cyanobacterial strain (Synechococcus 2973-T) that is capable of undergoing natural transformation and has a replication time on par with that of the fastest-growing cyanobacterium discovered to date. This new cyanobacterium has the potential to serve as a new model organism for the cyanobacterial research community and will allow experiments to be completed in a fraction of the time it has taken to complete previous assays.

Systematic Engineering of Synechococcus elongatus UTEX 2973 for Photosynthetic Production of l-Lysine, Cadaverine, and Glutarate

Amino acids and related targets are typically produced by well-characterized heterotrophs including Corynebacterium glutamicum and Escherichia coli. Cyanobacteria offer an opportunity to supplant these sugar-intensive processes by instead directly utilizing atmospheric CO₂ and sunlight. Synechococcus elongatus UTEX 2973 (hereafter UTEX 2973) is a particularly promising photoautotrophic platform due to its fast growth rate. Here, we first engineered UTEX 2973 to overproduce l-lysine (hereafter lysine), after which both cadaverine and glutarate production were achieved through further pathway engineering. To facilitate metabolic engineering, the relative activities of a subset of previously uncharacterized promoters were investigated, in each case, while also comparing the effects of both chromosomal (from neutral site NS3) and episomal (from pAM4788) expressions. Using these parts, lysine overproduction in UTEX 2973 was engineered by introducing a feedback-resistant copy of aspartate kinase (encoded by lysC^fbr) and a lysine exporter (encoded by ybjE), both from E. coli. While chromosomal expression resulted in lysine production up to just 325.3 ± 14.8 mg/L after 120 h, this was then increased to 556.3 ± 62.3 mg/L via plasmid-based expression, also surpassing prior reports of photoautotrophic lysine bioproduction. Lastly, additional products of interest were then targeted by modularly extending the lysine pathway to glutarate and cadaverine, two 5-carbon, bioplastic monomers. By this approach, glutarate has so far been produced at final titers reaching 67.5 ± 2.2 mg/L by 96 h, whereas cadaverine has been produced at up to 55.3 ± 6.7 mg/L. Overcoming pathway and/or transport bottlenecks, meanwhile, will be important to improving upon these initial outputs.

Development of CRISPR-Cas9 knock-in tools for free fatty acid production using the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973

Synechococcus elongatus UTEX 2973 has one of the fastest measured doubling time of cyanobacteria making it an important candidate for metabolic engineering. Traditional genetic engineering methods, which rely on homologous recombination, however, are inefficient, labor-intensive, and time-consuming due to the oligoploidy or polyploidy nature of cyanobacteria and the reliance on unique antibiotic resistance markers. CRISPR-Cas9 has emerged as an effective and versatile editing platform in a wide variety of organisms, but its application for cyanobacterial engineering is limited by the inherent toxicity of Cas9 resulting in poor transformation efficiencies. Here, we demonstrated that a single-plasmid CRISPR-Cas9 system, pCRISPOmyces-2, can effectively knock-in a truncated thioesterase gene from Escherichia coli to generate free fatty acid (FFA) producing mutants of Syn2973. To do so, three parameters were evaluated on the effect of generating recipient colonies after conjugation with pCRISPOmyces-2-based plasmids: 1) a modified conjugation protocol termed streaked conjugation, 2) the deletion of the gene encoding RecJ exonuclease, and 3) single guide RNA (sgRNA) sequence. With the use of the streaked conjugation protocol and a ΔrecJ mutant strain of Syn2973, the conjugation efficiency for the pCRISPomyces-2 plasmid could be improved by 750-fold over the wildtype (WT) for a conjugation efficiency of 2.0 × 10^-6 transconjugants/recipient cell. While deletion of the RecJ exonuclease alone increased the conjugation efficiency by 150-fold over the WT, FFA generation was impaired in FFA-producing mutants with the ΔrecJ background, and the large number of poor FFA-producing isolates indicated the potential increase in spontaneous mutation rates. The sgRNA sequence was found to be critical in achieving the desired CRISPR-Cas9-mediated knock-in mutation as the sgRNA impacts conjugation efficiency, likelihood of homogenous recombinants, and free fatty acid production in engineered strains.

Debottlenecking Thermophilic Cyanobacteria Cultivation and Harvesting through the Application of Inner-Light Photobioreactor and Chitosan

Thermophilic cyanobacteria are a low-carbon environmental resource with high potential thanks to their innate temperature tolerance and thermostable pigment, phycocyanin, which enhances light utilisation efficiency and generates a high-value product. However, large-scale cultivation and harvesting have always been bottlenecks in unicellular cyanobacteria cultivation due to their micrometric size. In this study, a 40-litre inner-light photobioreactor (PBR) was designed for scaled-up cultivation of Thermosynechococcus elongatus E542. By analysing light transmission and attenuation in the PBR and describing it via mathematical models, the supply of light energy to the reactor was optimised. It was found that the hyperbolic model describes the light attenuation characteristics of the cyanobacterial culture more accurately than the Lambert-Beer model. The internal illumination mode was applied for strain cultivation and showed a two-fold better growth rate and four-fold higher biomass concentration than the same strain grown in an externally illuminated photobioreactor. Finally, the downstream harvesting process was explored. A mixture of chitosan solutions was used as a flocculant to facilitate biomass collection. The effect of the following parameters on biomass harvesting was analysed: solution concentration, flocculation time and flocculant concentration. The analysis revealed that a 4 mg L^-1 chitosan solution is optimal for harvesting the strain. The proposed solutions can improve large-scale cyanobacterial biomass cultivation and processing.

Synthetic counter-selection markers and their application in genetic modification of Synechococcus elongatus UTEX2973

Due to its robustness to environmental stresses and fast growth, Synechococcus elongatus UTEX2973 is developed as a new model for researches on cyanobacterial molecular biology and biotechnology. However, systematic genetic modifications of S. elongatus UTEX2973 were hindered by the lack of effective genetic manipulation tools, especially available counter-selection markers. Here, six synthetic counter-selection markers (SCOMs) were assembled by fusing six toxin genes from either Escherichia coli or cyanobacteria with a theophylline-inducible promoter. The SCOMs containing SYNPCC7002_G0085 from Synechococcus sp. PCC7002 or mazF from E. coli were proved to be inducible by theophylline in S. elongatus UTEX2973. By using the mazF-based SCOM, the neutral locus 1 and 23 small regulatory RNAs were completely deleted from the genome of S. elongatus UTEX2973 after one round of selection with both kanamycin and theophylline. The genetic tools developed in this work will facilitate future researches on molecular genetics and synthetic biology in S. elongatus UTEX2973. KEY POINTS: • Two inducible counter-selection markers are lethal to S. elongatus UTEX2973. • The counter-selection marker benefits the gene targeting in S. elongatus UTEX2973. • Twentry-three small regulatory RNAs were fully deleted via the novel gene targeting method.

Salt-Tolerant Synechococcus elongatus UTEX 2973 Obtained via Engineering of Heterologous Synthesis of Compatible Solute Glucosylglycerol

The recently isolated cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) is characterized by a faster growth rate and greater tolerance to high temperature and high light, making it a good candidate chassis for autotrophic photosynthetic microbial cell factories. However, Syn2973 is sensitive to salt stress, making it urgently important to improve the salt tolerance of Syn2973 for future biotechnological applications. Glucosylglycerol, a compatible solute, plays an important role in resisting salt stress in moderate and marine halotolerant cyanobacteria. In this study, the salt tolerance of Syn2973 was successfully improved by introducing the glucosylglycerol (GG) biosynthetic pathway (OD₇₅₀ improved by 24% at 60 h). In addition, the salt tolerance of Syn2973 was further enhanced by overexpressing the rate-limiting step of glycerol-3-phosphate dehydrogenase and downregulating the gene rfbA, which encodes UDP glucose pyrophosphorylase. Taken together, these results indicate that the growth of the end-point strain M-2522-GgpPS-drfbA was improved by 62% compared with the control strain M-pSI-pSII at 60 h under treatment with 0.5 M NaCl. Finally, a comparative metabolomic analysis between strains M-pSI-pSII and M-2522-GgpPS-drfbA was performed to characterize the carbon flux in the engineered M-2522-GgpPS-drfbA strain, and the results showed that more carbon flux was redirected from ADP-GLC to GG synthesis. This study provides important engineering strategies to improve salt tolerance and GG production in Syn2973 in the future.

Improved CO2-derived polyhydroxybutyrate (PHB) production by engineering fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 for potential utilization of flue gas

Industrial application of cyanobacterial poly-β-hydroxybutyrate (PHB) production from CO₂ is currently challenged by slow growth rate and low photoautotrophic PHB productivity of existing cyanobacteria species. Herein, a novel PHB-producing cyanobacterial strain was developed by harnessing fast-growing cyanobacteria Synechococcus elongatus UTEX 2973 with introduction of heterologous phaCAB genes. Under photoautotrophic condition, the engineered strain produced 420 mg L^-1 (16.7% of dry cell weight) with the highest specific productivity of 75.2 mg L^-1 d^-1. When compared with a native PHB producer Synechocystis PCC 6803 under nitrogen deprivation, the engineered strain exhibited 2.4-fold higher PHB productivity. The performance of the engineered strain was further demonstrated in large scale cultivation using photobioreactor and outdoor cultivation employing industrial flue gas as the sole carbon source. This study can provide a promising solution to address petroleum-based plastic waste and contribute to CO₂ mitigation.

The circadian rhythm regulator RpaA modulates photosynthetic electron transport and alters the preferable temperature range for growth in a cyanobacterium

Cyanobacterial strains can grow within a specific temperature range that approximately corresponds to their natural habitat. However, how the preferable temperature range for growth (PTRG) is determined at the molecular level remains unclear. In this study, we detected a PTRG upshift in a mutant strain of Synechococcus elongatus PCC 7942 lacking the circadian rhythm regulator RpaA. Subsequent analyses revealed that RpaA decreases the electron transport from photosystem I to NADPH. The change in electron transport likely inhibits H₂ O₂ generation under high-temperature conditions and contributes to the observed PTRG upshift in rpaA-deficient cells. The importance of the effects of the circadian rhythm regulator on the PTRG is discussed.

Engineering Photosynthetic Bioprocesses for Sustainable Chemical Production: A Review

Microbial production of chemicals using renewable feedstocks such as glucose has emerged as a green alternative to conventional chemical production processes that rely primarily on petroleum-based feedstocks. The carbon footprint of such processes can further be reduced by using engineered cells that harness solar energy to consume feedstocks traditionally considered to be wastes as their carbon sources. Photosynthetic bacteria utilize sophisticated photosystems to capture the energy from photons to generate reduction potential with such rapidity and abundance that cells often cannot use it fast enough and much of it is lost as heat and light. Engineering photosynthetic organisms could enable us to take advantage of this energy surplus by redirecting it toward the synthesis of commercially important products such as biofuels, bioplastics, commodity chemicals, and terpenoids. In this work, we review photosynthetic pathways in aerobic and anaerobic bacteria to better understand how these organisms have naturally evolved to harness solar energy. We also discuss more recent attempts at engineering both the photosystems and downstream reactions that transfer reducing power to improve target chemical production. Further, we discuss different methods for the optimization of photosynthetic bioprocess including the immobilization of cells and the optimization of light delivery. We anticipate this review will serve as an important resource for future efforts to engineer and harness photosynthetic bacteria for chemical production.

Enhanced limonene production in a fast-growing cyanobacterium through combinatorial metabolic engineering

Terpenoids are a large and diverse group of natural products with commercial applications. Microbial production of terpenes is considered as a feasible approach for the stable supply of these complex hydrocarbons. Cyanobacteria, photosynthetic prokaryotes, are attractive hosts for sustainable bioproduction, because these autotrophs require only light and CO₂ for growth. Despite cyanobacteria having been engineered to produce a variety of compounds, their productivities of terpenes are generally low. Further research is needed to determine the bottleneck reactions for enhancing terpene production in cyanobacteria. In this study, we engineered the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 to produce a commercially-used terpenoid, limonene. We identified a beneficial mutation in the gene encoding geranylgeranyl pyrophosphate synthase crtE, leading to a 2.5-fold increase in limonene production. The engineered strain produced 16.4 ​mg ​L⁻¹ of limonene at a rate of 8.2 ​mg ​L⁻¹ day⁻¹, which is 8-fold higher than limonene productivities previously reported in other cyanobacterial species. Furthermore, we employed a combinatorial metabolic engineering approach to optimize genes involved in the upstream pathway of limonene biosynthesis. By modulating the expression of genes encoding the enzymes in the MEP pathway and the geranyl pyrophosphate synthase, we showed that optimization of the expression level is critical to enhance limonene production in cyanobacteria.

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Engineering of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973 for limonene production.

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Identification of a beneficial mutation with 2.5-fold increase in limonene productivity.

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Pathway optimization for limonene biosynthesis.

Trans-4-hydroxy-L-proline production by the cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria play an important role in photobiotechnology. Yet, one of their key central metabolic pathways, the tricarboxylic acid (TCA) cycle, has a unique architecture compared to most heterotrophs and still remains largely unexploited. The conversion of 2-oxoglutarate to succinate via succinyl-CoA is absent but is by-passed by several other reactions. Overall, fluxes under photoautotrophic growth conditions through the TCA cycle are low, which has implications for the production of chemicals. In this study, we investigate the capacity of the TCA cycle of Synechocystis sp PCC 6803 for the production of trans-4-hydroxy-L-proline (Hyp), a valuable chiral building block for the pharmaceutical and cosmetic industries. For the first time, photoautotrophic Hyp production was achieved in a cyanobacterium expressing the gene for the L-proline-4-hydroxylase (P4H) from Dactylosporangium sp. strain RH1. Interestingly, while elevated intracellular Hyp concentrations could be detected in the recombinant Synechocystis strains under all tested conditions, detectable Hyp secretion into the medium was only observed when the pH of the medium exceeded 9.5 and mostly in the late phases of the cultivation. We compared the rates obtained for autotrophic Hyp production with published sugar-based production rates in E. coli. The land-use efficiency (space-time yield) of the phototrophic process is already in the same order of magnitude as the heterotrophic process considering sugar farming as well. But, the remarkable plasticity of the cyanobacterial TCA cycle promises the potential for a 23–55 fold increase in space-time yield when using Synechocystis. Altogether, these findings contribute to a better understanding of bioproduction from the TCA cycle in photoautotrophs and broaden the spectrum of chemicals produced in metabolically engineered cyanobacteria.

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Phototrophic production of trans-4-hydroxy-L-prolin.

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pH dependency of product accumulation in Synechocystis PCC6803.

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Comparative analysis of land use efficiency in phototrophs & heterotrophs.

Engineering biology approaches for food and nutrient production by cyanobacteria

As photoautotrophic organisms, cyanobacteria capture and store solar energy in the form of biomass. Cyanobacterial biomass has been an important component of diet and nutrition in several regions for centuries. Synthetic biology strategies are currently being applied to increase the yield and productivity of cyanobacterial biomass by optimizing solar energy utilization and CO₂ fixation rates for carbon storage. Likewise, engineering cyanobacteria as cellular factories to synthesize carbohydrates, amino acids, proteins, lipids and fatty acids is providing an attractive way to sustainably produce food and nutrients for human consumption. In this review, we have summarized recent progress in both aspects and prospective trends under development.

Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia

Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081^T (= CBAS 745^T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081^T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.

High Light Induced Alka(e)ne Biodegradation for Lipid and Redox Homeostasis in Cyanobacteria

Cyanobacteria are the oldest photosynthetic microorganisms with good environmental adaptability. They are ubiquitous in light-exposed habitats on Earth. In recent years, cyanobacteria have become an ideal platform for producing biofuels and biochemicals from solar energy and carbon dioxide. Alka(e)nes are the main constituents of gasoline, diesel, and jet fuels. Alka(e)ne biosynthesis pathways are present in all sequenced cyanobacteria. Most cyanobacteria biosynthesize long chain alka(e)nes via acyl-acyl-carrier proteins reductase (AAR) and aldehyde-deformylating oxygenase (ADO). Alka(e)nes can be biodegraded by a variety of cyanobacteria, which lack a β-oxidation pathway. However, the mechanisms of alka(e)ne biodegradation in cyanobacteria remain elusive. In this study, a cyanobacterial alka(e)ne biodegradation pathway was uncovered by in vitro enzyme assays. Under high light, alka(e)nes in the membrane can be converted into alcohols and aldehydes by ADO, and aldehyde dehydrogenase (ALDH) can then convert the aldehydes into fatty acids to maintain lipid homeostasis in cyanobacteria. As highly reduced molecules, alka(e)nes could serve as electron donors to further reduce partially reduced reactive oxygen species (ROS) in cyanobacteria under high light. Alka(e)ne biodegradation may serve as an emergency mechanism for responding to the oxidative stress generated by excess light exposure. This study will shed new light on the roles of alka(e)ne metabolism in cyanobacteria. It is important to reduce the content of ROS by optimization of cultivation and genetic engineering for efficient alka(e)ne biosynthesis in cyanobacteria.

Extremophile Microalgae: the potential for biotechnological application

Microalgae are photosynthetic microorganisms that use sunlight as an energy source, and convert water, carbon dioxide, and inorganic salts into algal biomass. The isolation and selection of microalgae, which allow one to obtain large amounts of biomass and valuable compounds, is a prerequisite for their successful industrial production. This work provides an overview of extremophile algae, where their ability to grow under harsh conditions and the corresponding accumulation of metabolites are addressed. Emphasis is placed on the high-value products of some prominent algae. Moreover, the most recent applications of these microorganisms and their potential exploitation in the context of astrobiology are taken into account.

Opportunities toward hydrogen production biotechnologies

Hydrogen is already a major commodity and process intermediate for fertilizer production, petroleum processing, and chemical synthesis. It also offers unrealized potential for energy storage. While biological production offers an expandable and sustainable source, enthusiasm has been dampened by slow research progress. Also, the very low cost of natural gas (the major current hydrogen source) imposes severe economic challenges. This discussion describes process, metabolic, and protein engineering opportunities toward cost-effective biohydrogen production. Recent progress in hydrogenase engineering and photosynthetic bacterial research now suggests a favorable risk versus reward opportunity. Although the risks are still significant, successful technologies would provide important components in an integrated energy portfolio that enables global sustainability.

Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes

Cyanobacteria are model organisms for photosynthesis and are attractive for biotechnology applications. To aid investigation of genotype-phenotype relationships in cyanobacteria, we develop an inducible CRISPRi gene repression library in Synechocystis sp. PCC 6803, where we aim to target all genes for repression. We track the growth of all library members in multiple conditions and estimate gene fitness. The library reveals several clones with increased growth rates, and these have a common upregulation of genes related to cyclic electron flow. We challenge the library with 0.1 M L-lactate and find that repression of peroxiredoxin bcp2 increases growth rate by 49%. Transforming the library into an L-lactate-secreting Synechocystis strain and sorting top lactate producers enriches clones with sgRNAs targeting nutrient assimilation, central carbon metabolism, and cyclic electron flow. In many examples, productivity can be enhanced by repression of essential genes, which are difficult to access by transposon insertion.

Tunable Repression of Key Photosynthetic Processes Using Cas12a CRISPR Interference in the Fast-Growing Cyanobacterium Synechococcus sp. UTEX 2973

Cyanobacteria are photoautotrophic prokaryotes that serve as key model organisms to study basic photosynthetic processes and are potential carbon-negative production chassis for commodity and high-value chemicals. The development of new synthetic biology tools and improvement of current ones is a requisite for furthering these organisms as models and production vehicles. CRISPR interference (CRISPRi) allows for targeted gene repression using a DNase-dead Cas nuclease ("dCas"). Here, we describe a titratable dCas12a (dCpf1) CRISPRi system and apply it to repress key photosynthetic processes in the fast-growing cyanobacterium Synechococcus sp. UTEX 2973 (S2973). The system relies on a lac repressor system that retains tight regulation in the absence of inducer (0-10% repression) while maintaining the capability for >90% repression of high-abundance gene targets. We determined that dCas12a is less toxic than dCas9. We tested the efficacy of the system toward eYFP and three native targets in S2973: the phycobilisome antenna, glycogen synthesis, and photosystem I (PSI), an essential part of the photosynthetic electron transport chain in oxygenic photoautotrophs. PSI was knocked down indirectly by repressing the protein factor BtpA involved in stabilizing core PSI proteins. We could reduce cellular PSI titer by 87% under photoautotrophic conditions, and we characterized these cells to gain insights into the response of the strain to the low PSI content. The ability to tightly regulate and time the (de)repression of essential genes in trans will allow for the study of photosynthetic processes that are not accessible using knockout mutants.

Enhanced production of sucrose in the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

Cyanobacteria are attractive microbial hosts for production of chemicals using light and CO2. However, their low productivity of chemicals is a major challenge for commercial applications. This is mostly due to their relatively slow growth rate and carbon partitioning toward biomass rather than products. Many cyanobacterial strains synthesize sucrose as an osmoprotectant to cope with salt stress environments. In this study, we harnessed the photosynthetic machinery of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 to produce sucrose under salt stress conditions and investigated if the high efficiency of photosynthesis can enhance the productivity of sucrose. By expressing the sucrose transporter CscB, Synechococcus 2973 produced 8 g L-1 of sucrose with a highest productivity of 1.9 g L-1 day-1 under salt stress conditions. The salt stress activated the sucrose biosynthetic pathway mostly via upregulating the sps gene, which encodes the rate-limiting sucrose-phosphate synthase enzyme. To alleviate the demand on high concentrations of salt for sucrose production, we further overexpressed the sucrose synthesis genes in Synechococcus 2973. The engineered strain produced sucrose with a productivity of 1.1 g L-1 day-1 without the need of salt induction. The engineered Synechococcus 2973 in this study demonstrated the highest productivity of sucrose in cyanobacteria.

Flux balance analysis of cyanobacteria reveals selective use of photosynthetic electron transport components under different spectral light conditions

Cyanobacteria acclimate and adapt to changing light conditions by controlling the energy transfer between photosystem I (PSI) and II (PSII) and pigment composition. Photosynthesis is driven by balancing the excitation between PSI and PSII. To predict the detailed electron transfer flux of cyanobacteria, we refined the photosynthesis-related reactions in our previously reconstructed genome-scale model. Two photosynthetic bacteria, Arthrospira and Synechocystis, were used as models. They were grown under various spectral light conditions and flux balance analysis (FBA) was performed using photon uptake fluxes into PSI and PSII, which were converted from each light spectrum by considering the photoacclimation of pigments and the distribution ratio of phycobilisome to PSI and PSII. In Arthrospira, the FBA was verified with experimental data using six types of light-emitting diodes (White, Blue, Green, Yellow, Red1, and Red2). FBA predicted the cell growth of Synechocystis for the LEDs, excepting Red2. In an FBA simulation, cells used respiratory terminal oxidases and two NADH dehydrogenases (NDH-1 and NDH-2) to balance the PSI and PSII excitations depending on the light conditions. FBA simulation with our refined model functionally implicated NDH-1 and NDH-2 as a component of cyclic electron transport in the varied light environments.