Design, engineering, and construction of photosynthetic microbial cell factories for renewable solar fuel production

Toward combined photobiological-photochemical formation of kerosene-type biofuels: which small 1,3-diene photodimerizes most efficiently?

A transition from fossil- to bio-based hydrocarbon fuels is required to reduce greenhouse gas emissions; yet, traditional biomass cultivation for biofuel production competes with food production and impacts negatively on biodiversity. Recently, we reported a proof-of-principle study of a two-step photobiological-photochemical approach to kerosene biofuels in which a volatile hydrocarbon (isoprene) is produced by photosynthetic cyanobacteria, followed by its photochemical dimerization into C₁₀ hydrocarbons. Both steps can utilize solar irradiation. Here, we report the triplet state (T₁)-sensitized photodimerization of a broader set of small 1,3-dienes to identify which structural features lead to rapid photodimerization. Neat 1,3-cyclohexadiene gave the highest yield (93%) after 24 h of irradiation at 365 nm, followed by isoprene (66%). The long triplet lifetime of 1,3-cyclohexadiene, which is two orders of magnitude longer than those of acyclic dienes, is key to its high photoreactivity and stem from its planar T₁ state structure. In contrast, while isoprene is conformationally flexible, it has both photochemical and photobiological advantages, as it is the most reactive among the volatile 1,3-dienes and it can be produced by cyanobacteria. Finally, we explored the influence of solvent viscosity, diene concentration, and triplet sensitizer loading on the photodimerization, with a focus on conditions that are amenable when the dienes are produced photobiologically. Our findings should be useful for the further development of the two-step photobiological-photochemical approach to kerosene biofuels.

Increased ethylene production by overexpressing phosphoenolpyruvate carboxylase in the cyanobacterium Synechocystis PCC 6803

BACKGROUND

Cyanobacteria can be metabolically engineered to convert CO₂ to fuels and chemicals such as ethylene. A major challenge in such efforts is to optimize carbon fixation and partition towards target molecules.

RESULTS

The efe gene encoding an ethylene-forming enzyme was introduced into a strain of the cyanobacterium Synechocystis PCC 6803 with increased phosphoenolpyruvate carboxylase (PEPc) levels. The resulting engineered strain (CD-P) showed significantly increased ethylene production (10.5 ± 3.1 µg mL^-1 OD^-1 day^-1) compared to the control strain (6.4 ± 1.4 µg mL^-1 OD^-1 day^-1). Interestingly, extra copies of the native pepc or the heterologous expression of PEPc from the cyanobacterium Synechococcus PCC 7002 (Synechococcus) in the CD-P, increased ethylene production (19.2 ± 1.3 and 18.3 ± 3.3 µg mL^-1 OD^-1 day^-1, respectively) when the cells were treated with the acetyl-CoA carboxylase inhibitor, cycloxydim. A heterologous expression of phosphoenolpyruvate synthase (PPSA) from Synechococcus in the CD-P also increased ethylene production (16.77 ± 4.48 µg mL^-1 OD^-1 day^-1) showing differences in the regulation of the native and the PPSA from Synechococcus in Synechocystis.

CONCLUSIONS

This work demonstrates that genetic rewiring of cyanobacterial central carbon metabolism can enhance carbon supply to the TCA cycle and thereby further increase ethylene production.

Cyanobacteria as an eco-friendly resource for biofuel production: A critical review

Cyanobacteria are photosynthetic microorganisms which can be found in various environmental habitats. These photosynthetic bacteria are considered as promising feedstock for the production of the third- and the fourth-generation biofuels. The main subject of this review is highlighting the significant aspects of the biofuel production from cyanobacteria. The most recent investigations about the extraction or separation of the bio-oil from cyanobacteria are also adduced in the present review. Moreover, the genetic engineering of cyanobacteria for improving biofuel production and the impact of bioinformatics studies on the designing better-engineered strains are mentioned. The large-scale biofuel production is challenging, so the economic considerations to provide inexpensive biofuels are also cited. It seems that the future of biofuels is strongly dependent to the following items; understanding the metabolic pathways of the cyanobacterial species, progression in the construction of the engineered cyanobacteria, and inexpensive large-scale cultivation of them.

Expanding the toolbox for Synechocystis sp. PCC 6803: validation of replicative vectors and characterization of a novel set of promoters

Cyanobacteria are promising 'low-cost' cell factories since they have minimal nutritional requirements, high metabolic plasticity and can use sunlight and CO₂ as energy and carbon sources. The unicellular Synechocystis sp. PCC 6803, already considered the 'green' Escherichia coli, is the best studied cyanobacterium but to be used as an efficient and robust photoautotrophic chassis it requires a customized and well-characterized toolbox. In this context, we evaluated the possibility of using three self-replicative vectors from the Standard European Vector Architecture (SEVA) repository to transform Synechocystis. Our results demonstrated that the presence of the plasmid does not lead to an evident phenotype or hindered Synechocystis growth, being the vast majority of the cells able to retain the replicative plasmid even in the absence of selective pressure. In addition, a set of heterologous and redesigned promoters were characterized exhibiting a wide range of activities compared to the reference P _rnpB , three of which could be efficiently repressed. As a proof-of-concept, from the expanded toolbox, one promoter was selected and assembled with the ggpS gene [encoding one of the proteins involved in the synthesis of the native compatible solute glucosylglycerol (GG)] and the synthetic device was introduced into Synechocystis using one of the SEVA plasmids. The presence of this device restored the production of the GG in a ggpS deficient mutant validating the functionality of the tools/device developed in this study.

Construction of a Shuttle Vector Using an Endogenous Plasmid From the Cyanobacterium Synechocystis sp. PCC6803

To advance synthetic biology in the photosynthetic cyanobacterium Synechocystis sp. PCC6803 (Syn6803), we constructed a shuttle vector with some versatile features. This shuttle vector, pSCB-YFP, consists of a putative replicon identified on the plasmid pCC5.2, the origin of replication of pMB1 from E. coli, as well as the YFP reporter gene and a spectinomycin/streptomycin resistance cassette. pSCB-YFP is stably maintained in Syn6803M (a motile strain that lacks the endogenous pCC5.2) and expresses YFP. In addition, we engineered a fragment into pSCB-YFP that has multiple cloning sites and other features such that this plasmid can also be used as an expression vector (pSCBe). The shuttle vector pSCB-YFP can be stably maintained for at least 50 generations without antibiotic selection. It is a high copy number plasmid and can stably co-exist with the RSF1010-based pPMQAK1-GFP.

Harnessing transcription for bioproduction in cyanobacteria

Sustainable production of biofuels and other valuable compounds is one of our future challenges. One tempting possibility is to use photosynthetic cyanobacteria as production factories. Currently, tools for genetic engineering of cyanobacteria are not good enough to exploit the full potential of cyanobacteria. A wide variety of expression systems will be required to adjust both the expression of heterologous enzyme(s) and metabolic routes to the best possible balance, allowing the optimal production of a particular substance. In bacteria, transcription, especially the initiation of transcription, has a central role in adjusting gene expression and thus also metabolic fluxes of cells according to environmental cues. Here we summarize the recent progress in developing tools for efficient cyanofactories, focusing especially on transcriptional regulation.

Fabrication of Photoreactive Biocomposite Coatings via Electric Field-Assisted Assembly of Cyanobacteria

We report how dielectrophoresis (DEP) can be used as a tool for the fabrication of biocomposite coatings of photoreactive cyanobacteria (Synechococcus PCC7002) on flexible polyester sheets (PEs). The PE substrates were precoated by a layer-by-layer assembled film of charged polyelectrolytes. In excellent agreement between experimental data and numerical simulations, the directed assembly process driven by external electric field results in the formation of 1D chains and 2D sheets by the cells. The preassembled cyanobacteria chains and arrays became deposited on the substrate and remained in place after the electric field was turned off due to the electrostatic attraction between the negatively charged cell surfaces and the positively charged polyelectrolyte-coated PE. The DEP-assisted packing of cyanobacteria is close to the maximal surface coverage of ∼70% estimated from convectively assembled monolayers. Confocal laser scanning microscopy and spectrophotometry confirm that the photosynthetic pigment integrity of the Synechococcus cells is preserved after DEP immobilization. The significant decrease of the light scattering and the enhanced transmittance of these field-assembled cyanobacteria coatings demonstrate reduced self-shading compared to suspension cultures. Thus, we achieved the assembly of structured cyanobacteria coatings that optimize cell surface coverage and preserve cell viability after immobilization. This is a step toward the development of flexible multilayered cell-based photoabsorbing biomaterials that can serve as components of "biomimetic leaves" for utilizing solar energy to recycle CO₂ into fuels or chemicals.

Artificial photosynthesis: closing remarks

This paper derives from my closing remarks lecture at the 198^th Faraday Discussion meeting on Artificial Photosynthesis, Kyoto, Japan, February 28–March 2. The meeting had sessions on biological approaches and fundamental processes, molecular catalysts, inorganic assembly catalysts, and integration of systems for demonstrating realistic devices. The field has had much progress since the previous Faraday Discussion on Artificial Photosynthesis in Edinburgh, UK, in 2011. This paper is a personal account of recent discussions and developments in the field, as reflected in and discussed during the meeting. First it discusses the general directions of artificial photosynthesis and some considerations for a future solar fuels technology. Then it comments on some scientific directions in the area of the meeting.

Proteomics dedicated to biofilmology: What have we learned from a decade of research?

Advances in proteomics techniques over the past decade, closely integrated with genomic and physicochemical approach, have played a great role in developing knowledge of the biofilm lifestyle of bacteria. Despite bacterial proteome versatility, many studies have demonstrated the ability of proteomics approaches to elucidating the biofilm phenotype. Though these investigations have been largely used for biofilm studies in the last decades, they represent, however, a very low percentage of proteomics works performed up to now. Such approaches have offered new targets for combating microbial biofilms by providing a comprehensive quantitative and qualitative overview of their protein cell content. Herein, we summarized the state of the art in knowledge about biofilm physiology after one decade of proteomic analysis. In a second part, we highlighted missing research tracks for the next decade, emphasizing the emergence of posttranslational modifications in proteomic studies stemming from recent advances in mass spectrometry-based proteomics.

Cyanobacterial hydrogenases and hydrogen metabolism revisited: recent progress and future prospects

Cyanobacteria have garnered interest as potential cell factories for hydrogen production. In conjunction with photosynthesis, these organisms can utilize inexpensive inorganic substrates and solar energy for simultaneous biosynthesis and hydrogen evolution. However, the hydrogen yield associated with these organisms remains far too low to compete with the existing chemical processes. Our limited understanding of the cellular hydrogen production pathway is a primary setback in the potential scale-up of this process. In this regard, the present review discusses the recent insight around ferredoxin/flavodoxin as the likely electron donor to the bidirectional Hox hydrogenase instead of the generally accepted NAD(P)H. This may have far reaching implications in powering solar driven hydrogen production. However, it is evident that a successful hydrogen-producing candidate would likely integrate enzymatic traits from different species. Engineering the [NiFe] hydrogenases for optimal catalytic efficiency or expression of a high turnover [FeFe] hydrogenase in these photo-autotrophs may facilitate the development of strains to reach target levels of biohydrogen production in cyanobacteria. The fundamental advancements achieved in these fields are also summarized in this review.

How close we are to achieving commercially viable large-scale photobiological hydrogen production by cyanobacteria: a review of the biological aspects

Photobiological production of H₂ by cyanobacteria is considered to be an ideal source of renewable energy because the inputs, water and sunlight, are abundant. The products of photobiological systems are H₂ and O₂; the H₂ can be used as the energy source of fuel cells, etc., which generate electricity at high efficiencies and minimal pollution, as the waste product is H₂O. Overall, production of commercially viable algal fuels in any form, including biomass and biodiesel, is challenging, and the very few systems that are operational have yet to be evaluated. In this paper we will: briefly review some of the necessary conditions for economical production, summarize the reports of photobiological H₂ production by cyanobacteria, present our schemes for future production, and discuss the necessity for further progress in the research needed to achieve commercially viable large-scale H₂ production.

The Anabaena sp. PCC 7120 Exoproteome: Taking a Peek outside the Box

The interest in examining the subset of proteins present in the extracellular milieu, the exoproteome, has been growing due to novel insights highlighting their role on extracellular matrix organization and biofilm formation, but also on homeostasis and development. The cyanobacterial exoproteome is poorly studied, and the role of cyanobacterial exoproteins on cell wall biogenesis, morphology and even physiology is largely unknown. Here, we present a comprehensive examination of the Anabaena sp. PCC 7120 exoproteome under various growth conditions. Altogether, 139 proteins belonging to 16 different functional categories have been identified. A large fraction (48%) of the identified proteins is classified as "hypothetical", falls into the "other categories" set or presents no similarity to other proteins. The evidence presented here shows that Anabaena sp. PCC 7120 is capable of outer membrane vesicle formation and that these vesicles are likely to contribute to the exoproteome profile. Furthermore, the activity of selected exoproteins associated with oxidative stress has been assessed, suggesting their involvement in redox homeostasis mechanisms in the extracellular space. Finally, we discuss our results in light of other cyanobacterial exoproteome studies and focus on the potential of exploring cyanobacteria as cell factories to produce and secrete selected proteins.

Survival strategies in the aquatic and terrestrial world: the impact of second messengers on cyanobacterial processes

Second messengers are intracellular substances regulated by specific external stimuli globally known as first messengers. Cells rely on second messengers to generate rapid responses to environmental changes and the importance of their roles is becoming increasingly realized in cellular signaling research. Cyanobacteria are photooxygenic bacteria that inhabit most of Earth's environments. The ability of cyanobacteria to survive in ecologically diverse habitats is due to their capacity to adapt and respond to environmental changes. This article reviews known second messenger-controlled physiological processes in cyanobacteria. Second messengers used in these systems include the element calcium (Ca2+), nucleotide-based guanosine tetraphosphate or pentaphosphate (ppGpp or pppGpp, represented as (p)ppGpp), cyclic adenosine 3',5'-monophosphate (cAMP), cyclic dimeric GMP (c-di-GMP), cyclic guanosine 3',5'-monophosphate (cGMP), and cyclic dimeric AMP (c-di-AMP), and the gaseous nitric oxide (NO). The discussion focuses on processes central to cyanobacteria, such as nitrogen fixation, light perception, photosynthesis-related processes, and gliding motility. In addition, we address future research trajectories needed to better understand the signaling networks and cross talk in the signaling pathways of these molecules in cyanobacteria. Second messengers have significant potential to be adapted as technological tools and we highlight possible novel and practical applications based on our understanding of these molecules and the signaling networks that they control.

The Regulation of Light Sensing and Light-Harvesting Impacts the Use of Cyanobacteria as Biotechnology Platforms

Light is harvested in cyanobacteria by chlorophyll-containing photosystems embedded in the thylakoid membranes and phycobilisomes (PBSs), photosystem-associated light-harvesting antennae. Light absorbed by the PBSs and photosystems can be converted to chemical energy through photosynthesis. Photosynthetically fixed carbon pools, which are constrained by photosynthetic light capture versus the dissipation of excess light absorbed, determine the available organismal energy budget. The molecular bases of the environmental regulation of photosynthesis, photoprotection, and photomorphogenesis are still being elucidated in cyanobacteria. Thus, the potential impacts of these phenomena on the efficacy of developing cyanobacteria as robust biotechnological platforms require additional attention. Current advances and persisting needs for developing cyanobacterial production platforms that are related to light sensing and harvesting include the development of tools to balance the utilization of absorbed photons for conversion to chemical energy and biomass versus light dissipation in photoprotective mechanisms. Such tools can be used to direct energy to more effectively support the production of desired bioproducts from sunlight.

Design and analysis of LacI-repressed promoters and DNA-looping in a cyanobacterium

BACKGROUND

Cyanobacteria are solar-powered prokaryotes useful for sustainable production of valuable molecules, but orthogonal and regulated promoters are lacking. The Lac repressor (LacI) from Escherichia coli is a well-studied transcription factor that is orthogonal to cyanobacteria and represses transcription by binding a primary lac operator (lacO), blocking RNA-polymerase. Repression can be enhanced through DNA-looping, when a LacI-tetramer binds two spatially separated lacO and loops the DNA. Ptrc is a commonly used LacI-repressed promoter that is inefficiently repressed in the cyanobacterium Synechocystis PCC 6803. Ptrc2O, a version of Ptrc with two lacO, is more efficiently repressed, indicating DNA-looping. To investigate the inefficient repression of Ptrc and cyanobacterial DNA-looping, we designed a Ptrc-derived promoter library consisting of single lacO promoters, including a version of Ptrc with a stronger lacO (Ptrc1O-proximal), and dual lacO promoters with varying inter-lacO distances (the Ptrc2O-library).

RESULTS

We first characterized artificial constitutive promoters and used one for engineering a LacI-expressing strain of Synechocystis. Using this strain, we observed that Ptrc1O-proximal is similar to Ptrc in being inefficiently repressed. Further, the Ptrc2O-library displays a periodic repression pattern that remains for both non- and induced conditions and decreases with longer inter-lacO distances, in both E. coli and Synechocystis. Repression of Ptrc2O-library promoters with operators out of phase is less efficient in Synechocystis than in E. coli, whereas repression of promoters with lacO in phase is efficient even under induced conditions in Synechocystis. Two well-repressed Ptrc2O promoters were highly active when tested in absence of LacI in Synechocystis.

CONCLUSIONS

The artificial constitutive promoters herein characterized can be utilized for expression in cyanobacteria, as demonstrated for LacI. The inefficient repression of Ptrc and Ptrc1O-proximal in Synechocystis, as compared to E. coli, may be due to insufficient LacI expression, or differences in RNAP subunits. DNA-looping works as a transcriptional regulation mechanism similarly as in E. coli. DNA-looping contributes strongly to Ptrc2O-library repression in Synechocystis, even though they contain the weakly-repressed primary lacO of Ptrc1O-proximal and relatively low levels of LacI/cell. Hence, Synechocystis RNAP may be more sensitive to DNA-looping than E. coli RNAP, and/or the chromatin torsion resistance could be lower. Two strong and highly repressed Ptrc2O promoters could be used without induction, or together with an unstable LacI.

Metabolic engineering of biosynthetic pathway for production of renewable biofuels

Metabolic engineering is an important area of research that involves editing genetic networks to overproduce a certain substance by the cells. Using a combination of genetic, metabolic, and modeling methods, useful substances have been synthesized in the past at industrial scale and in a cost-effective manner. Currently, metabolic engineering is being used to produce sufficient, economical, and eco-friendly biofuels. In the recent past, a number of efforts have been made towards engineering biosynthetic pathways for large scale and efficient production of biofuels from biomass. Given the adoption of metabolic engineering approaches by the biofuel industry, this paper reviews various approaches towards the production and enhancement of renewable biofuels such as ethanol, butanol, isopropanol, hydrogen, and biodiesel. We have also identified specific areas where more work needs to be done in the future.

Inactivation of uptake hydrogenase leads to enhanced and sustained hydrogen production with high nitrogenase activity under high light exposure in the cyanobacterium Anabaena siamensis TISTR 8012

BACKGROUND

Biohydrogen from cyanobacteria has attracted public interest due to its potential as a renewable energy carrier produced from solar energy and water. Anabaena siamensis TISTR 8012, a novel strain isolated from rice paddy field in Thailand, has been identified as a promising cyanobacterial strain for use as a high-yield hydrogen producer attributed to the activities of two enzymes, nitrogenase and bidirectional hydrogenase. One main obstacle for high hydrogen production by A. siamensis is a light-driven hydrogen consumption catalyzed by the uptake hydrogenase. To overcome this and in order to enhance the potential for nitrogenase based hydrogen production, we engineered a hydrogen uptake deficient strain by interrupting hupS encoding the small subunit of the uptake hydrogenase.

RESULTS

An engineered strain lacking a functional uptake hydrogenase (∆hupS) produced about 4-folds more hydrogen than the wild type strain. Moreover, the ∆hupS strain showed long term, sustained hydrogen production under light exposure with 2-3 folds higher nitrogenase activity compared to the wild type. In addition, HupS inactivation had no major effects on cell growth and heterocyst differentiation. Gene expression analysis using RT-PCR indicates that electrons and ATP molecules required for hydrogen production in the ∆hupS strain may be obtained from the electron transport chain associated with the photosynthetic oxidation of water in the vegetative cells. The ∆hupS strain was found to compete well with the wild type up to 50 h in a mixed culture, thereafter the wild type started to grow on the relative expense of the ∆hupS strain.

CONCLUSIONS

Inactivation of hupS is an effective strategy for improving biohydrogen production, in rates and specifically in total yield, in nitrogen-fixing cultures of the cyanobacterium Anabaena siamensis TISTR 8012.

Redirecting the electron flow towards the nitrogenase and bidirectional Hox-hydrogenase by using specific inhibitors results in enhanced H2 production in the cyanobacterium Anabaena siamensis TISTR 8012

The inhibition of competitive metabolic pathways by various inhibitors in order to redirect electron flow towards nitrogenase and bidirectional Hox-hydrogenase was investigated in Anabaena siamensis TISTR 8012. Cells grown in BG11(0) supplemented with KCN, rotenone, DCMU, and DL-glyceraldehyde under light condition for 24 h showed enhanced H(2) production. Cells grown in BG11 medium showed only marginal H(2) production and its production was hardly increased by the inhibitors tested. H(2) production with either 20mM KCN or 50 μM DCMU in BG11(0) medium was 22 μmol H(2) mg chl a(-1) h(-1), threefold higher than the control. The increased H(2) production caused by inhibitors was consistent with the increase in the respective Hox-hydrogenase activities and nifD transcript levels, as well as the decrease in hupL transcript levels. The results suggested that interruption of metabolic pathways essential for growth could redirect electrons flow towards nitrogenase and bidirectional Hox-hydrogenase resulting in increased H(2) production.

Overview: capturing the sun for energy production

Solar energy has potential to provide a major part of our energy for our future, as heat, electricity, and fuels. Most solar technologies are still at the research and development stage, however. There is therefore a need for bold and enduring efforts in research, development and commercialization, including strategic legislative measures and infrastructure investments. This overview article serves as an introduction to the present Special Report, briefly outlining the potential, principles and possibilities as well as some of the challenges of solar energy conversion.