Natural transformation of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1: a simple and efficient method for gene transfer

Identification of acidic stress-responsive genes and acid tolerance engineering in Synechococcus elongatus PCC 7942

Cyanobacteria are excellent autotrophic photosynthetic chassis employed in synthetic biology, and previous studies have suggested that they have alkaline tolerance but low acid tolerance, significantly limiting their productivity as photosynthetic chassis and necessitating investigations into the acid stress resistance mechanism. In this study, differentially expressed genes were obtained by RNA sequencing-based comparative transcriptomic analysis under long-term acidic stress conditions and acidic shock treatment, in the model cyanobacterium Synechococcus elongatus PCC 7942. A pathway enrichment analysis revealed the upregulated and downregulated pathways during long-term acidic and shock stress treatment. The subsequent single gene knockout and phenotype analysis showed that under acidic stress conditions, the strains with chlL, chlN, pex, synpcc7942_2038, synpcc7942_1890, or synpcc7942_2547 knocked out grew worse than the wild type, suggesting their involvement in acid tolerance. This finding was further confirmed by introducing the corresponding genes back into the knockout mutant individually. Moreover, individual overexpression of the chlL and chlN genes in the wild type successfully improved the tolerance of S. elongatus PCC 7942 to acidic stress. This work successfully identified six genes involved in acidic stress responses, and overexpressing chIL or chIN individually successfully improved acid tolerance in S. elongatus PCC 7942, providing valuable information to better understand the acid resistance mechanism in S. elongatus PCC 7942 and novel insights into the robustness and tolerance engineering of cyanobacterial chassis. KEY POINTS: • DEGs were identified by RNA-seq based transcriptomics analysis in response to acidic stress in S. elongatus PCC 7942. • Six genes were identified to be involved in acid tolerance in S. elongatus PCC 7942. • Overexpression of chIL or chIN individually successfully improved the acid tolerance of S. elongatus PCC 7942.

Illuminating microbial mat assembly: Cyanobacteria and Chloroflexota cooperate to structure light-responsive biofilms

Microbial mats are stratified communities often dominated by unicellular and filamentous phototrophs within an exopolymer matrix. It is challenging to quantify the dynamic responses of community members in situ as they experience steep gradients and rapid fluctuations of light. To address this, we developed a binary consortium using two representative isolates from hot spring mats, the unicellular oxygenic phototrophic cyanobacterium Synechococcus OS-B' (Syn OS-B') and the filamentous anoxygenic phototroph Chloroflexus MS-CIW-1 (Chfl MS-1). We quantified the motility of individual cells and entire colonies and demonstrated that Chfl MS-1 formed bundles of filaments that moved in all directions with no directional bias to light. Syn OS- B' was slightly less motile but exhibited positive phototaxis. This binary consortium displayed cooperative behavior by moving further than either species alone and formed ordered arrays where both species aligned with the light source. No cooperative motility was observed when a non-motile pilB mutant of Syn OS-B' was used instead of Syn OS-B'. The binary consortium also produced more adherent biofilm than individual species, consistent with the close interspecies association revealed by electron microscopy. We propose that cyanobacteria and Chloroflexota cooperate in forming natural microbial mats, by colonizing new niches and building robust biofilms.

Thermophilic cyanobacteria-exciting, yet challenging biotechnological chassis

Thermophilic cyanobacteria are prokaryotic photoautotrophic microorganisms capable of growth between 45 and 73 °C. They are typically found in hot springs where they serve as essential primary producers. Several key features make these robust photosynthetic microbes biotechnologically relevant. These are highly stable proteins and their complexes, the ability to actively transport and concentrate inorganic carbon and other nutrients, to serve as gene donors, microbial cell factories, and sources of bioactive metabolites. A thorough investigation of the recent progress in thermophilic cyanobacteria reveals a significant increase in the number of newly isolated and delineated organisms and wide application of thermophilic light-harvesting components in biohybrid devices. Yet despite these achievements, there are still deficiencies at the high-end of the biotechnological learning curve, notably in genetic engineering and gene editing. Thermostable proteins could be more widely employed, and an extensive pool of newly available genetic data could be better utilised. In this manuscript, we attempt to showcase the most important recent advances in thermophilic cyanobacterial biotechnology and provide an overview of the future direction of the field and challenges that need to be overcome before thermophilic cyanobacterial biotechnology can bridge the gap with highly advanced biotechnology of their mesophilic counterparts. KEY POINTS: • Increased interest in all aspects of thermophilic cyanobacteria in recent years • Light harvesting components remain the most biotechnologically relevant • Lack of reliable molecular biology tools hinders further development of the chassis.

Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria

Cyanobacteria are photosynthetic microorganisms capable of using solar energy to convert CO2 and H2O into O2 and energy-rich organic compounds, thus enabling sustainable production of a wide range of bio-products. More and more strains of cyanobacteria are identified that show great promise as cell platforms for the generation of bioproducts. However, strain development is still required to optimize their biosynthesis and increase titers for industrial applications. This review describes the most well-known, newest and most promising strains available to the community and gives an overview of current cyanobacterial biotechnology and the latest innovative strategies used for engineering cyanobacteria. We summarize advanced synthetic biology tools for modulating gene expression and their use in metabolic pathway engineering to increase the production of value-added compounds, such as terpenoids, fatty acids and sugars, to provide a go-to source for scientists starting research in cyanobacterial metabolic engineering.

Natural Competence in the Filamentous, Heterocystous Cyanobacterium Chlorogloeopsis fritschii PCC 6912

Lateral gene transfer plays an important role in the evolution of genetic diversity in prokaryotes. DNA transfer via natural transformation depends on the ability of recipient cells to actively transport DNA from the environment into the cytoplasm, termed natural competence, which relies on the presence of type IV pili and other competence proteins. Natural competence has been described in cyanobacteria for several organisms, including unicellular and filamentous species. However, natural competence in cyanobacteria that differentiate specialized cells for N₂-fixation (heterocysts) and form branching or multiseriate cell filaments (termed subsection V) remains unknown. Here, we show that genes essential for natural competence are conserved in subsection V cyanobacteria. Furthermore, using the replicating plasmid pRL25C, we experimentally demonstrate natural competence in a subsection V organism: Chlorogloeopsis fritschii PCC 6912. Our results suggest that natural competence is a common trait in cyanobacteria forming complex cell filament morphologies.

IMPORTANCE Cyanobacteria are crucial players in the global biogeochemical cycles, where they contribute to CO₂- and N₂-fixation. Their main ecological significance is the primary biomass production owing to oxygenic photosynthesis. Cyanobacteria are a diverse phylum, in which the most complex species differentiate specialized cell types and form true-branching or multiseriate cell filament structures (termed subsection V cyanobacteria). These bacteria are considered a peak in the evolution of prokaryotic multicellularity. Among others, species in that group inhabit fresh and marine water habitats, soil, and extreme habitats such as thermal springs. Here, we show that the core genes required for natural competence are frequent in subsection V cyanobacteria and demonstrate for the first time natural transformation in a member of subsection V. The prevalence of natural competence has implications for the role of DNA acquisition in the genome evolution of cyanobacteria. Furthermore, the presence of mechanisms for natural transformation opens up new possibilities for the genetic modification of subsection V cyanobacteria.

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.

Doing synthetic biology with photosynthetic microorganisms

The use of photosynthetic microbes as synthetic biology hosts for the sustainable production of commodity chemicals and even fuels has received increasing attention over the last decade. The number of studies published, tools implemented, and resources made available for microalgae have increased beyond expectations during the last few years. However, the tools available for genetic engineering in these organisms still lag those available for the more commonly used heterotrophic host organisms. In this mini-review, we provide an overview of the photosynthetic microbes most commonly used in synthetic biology studies, namely cyanobacteria, chlorophytes, eustigmatophytes and diatoms. We provide basic information on the techniques and tools available for each model group of organisms, we outline the state-of-the-art, and we list the synthetic biology tools that have been successfully used. We specifically focus on the latest CRISPR developments, as we believe that precision editing and advanced genetic engineering tools will be pivotal to the advancement of the field. Finally, we discuss the relative strengths and weaknesses of each group of organisms and examine the challenges that need to be overcome to achieve their synthetic biology potential.

Structural insights into cyanobacterial photosystem II intermediates associated with Psb28 and Tsl0063

Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyses light-induced water oxidation, leading to the conversion of light energy into chemical energy and the release of dioxygen. We analysed the structures of two Psb28-bound PSII intermediates, Psb28-RC47 and Psb28-PSII, purified from a psbV-deletion strain of the thermophilic cyanobacterium Thermosynechococcus vulcanus, using cryo-electron microscopy. Both Psb28-RC47 and Psb28-PSII bind one Psb28, one Tsl0063 and an unknown subunit. Psb28 is located at the cytoplasmic surface of PSII and interacts with D1, D2 and CP47, whereas Tsl0063 is a transmembrane subunit and binds at the side of CP47/PsbH. Substantial structural perturbations are observed at the acceptor side, which result in conformational changes of the quinone (Q_B) and non-haem iron binding sites and thus may protect PSII from photodamage during assembly. These results provide a solid structural basis for understanding the assembly process of native PSII.

Heterologous production of cyanobacterial compounds

Cyanobacteria produce a plethora of compounds with unique chemical structures and diverse biological activities. Importantly, the increasing availability of cyanobacterial genome sequences and the rapid development of bioinformatics tools have unraveled the tremendous potential of cyanobacteria in producing new natural products. However, the discovery of these compounds based on cyanobacterial genomes has progressed slowly as the majority of their corresponding biosynthetic gene clusters (BGCs) are silent. In addition, cyanobacterial strains are often slow-growing, difficult for genetic engineering, or cannot be cultivated yet, limiting the use of host genetic engineering approaches for discovery. On the other hand, genetically tractable hosts such as Escherichia coli, Actinobacteria, and yeast have been developed for the heterologous expression of cyanobacterial BGCs. More recently, there have been increased interests in developing model cyanobacterial strains as heterologous production platforms. Herein, we present recent advances in the heterologous production of cyanobacterial compounds in both cyanobacterial and noncyanobacterial hosts. Emerging strategies for BGC assembly, host engineering, and optimization of BGC expression are included for fostering the broader applications of synthetic biology tools in the discovery of new cyanobacterial natural products.

Gene Delivery Technologies with Applications in Microalgal Genetic Engineering

Microalgae and cyanobacteria are photosynthetic microbes that can be grown with the simple inputs of water, carbon dioxide, (sun)light, and trace elements. Their engineering holds the promise of tailored bio-molecule production using sustainable, environmentally friendly waste carbon inputs. Although algal engineering examples are beginning to show maturity, severe limitations remain in the transformation of multigene expression cassettes into model species and DNA delivery into non-model hosts. This review highlights common and emerging DNA delivery methods used for other organisms that may find future applications in algal engineering.

Role of PsbV-Tyr137 in photosystem II studied by site-directed mutagenesis in the thermophilic cyanobacterium Thermosynechococcus vulcanus

PsbV (cytochrome c₅₅₀) is one of the three extrinsic proteins of photosystem II (PSII) and functions to maintain the stability and activity of the Mn₄CaO₅ cluster, the catalytic center for water oxidation. PsbV-Y137 is the C-terminal residue of PsbV and is located at the exit of a hydrogen-bond network mediated by the D1-Y161-H190 residue pair. In order to examine the function of PsbV-Y137, four mutants, PsbV-Y137A, PsbV-Y137F, PsbV-Y137G, and PsbV-Y137W, were generated with Thermosynechococcus vulcanus (T. vulcanus). These mutants showed growth rates similar to that of the wild-type strain (WT); however, their oxygen-evolving activities were different. At pH 6.5, the oxygen evolution rates of Y137F and Y137W were almost identical to that of WT, whereas the oxygen evolution rates of the Y137A, Y137G mutants were 64% and 61% of WT, respectively. However, the oxygen evolution in the latter two mutants decreased less at higher pHs, suggesting that higher pHs facilitated oxygen evolution probably by facilitating proton egress in these two mutants. Furthermore, thylakoid membranes isolated from the PsbV-Y137A, PsbV-Y137G mutants exhibited much lower levels of oxygen-evolving activity than that of WT, which was found to be caused by the release of PsbV. In addition, PSII complexes purified from the PsbV-Y137A and PsbV-Y137G mutants lost all of the three extrinsic proteins but instead bind Psb27, an assembly cofactor of PSII. These results demonstrate that the PsbV-Tyr137 residue is required for the stable binding of PsbV to PSII, and the hydrogen-bond network mediated by D1-Y161-H190 is likely to function in proton egress during water oxidation.

Function and Benefits of Natural Competence in Cyanobacteria: From Ecology to Targeted Manipulation

Natural competence is the ability of a cell to actively take up and incorporate foreign DNA in its own genome. This trait is widespread and ecologically significant within the prokaryotic kingdom. Here we look at natural competence in cyanobacteria, a group of globally distributed oxygenic photosynthetic bacteria. Many cyanobacterial species appear to have the genetic potential to be naturally competent, however, this ability has only been demonstrated in a few species. Reasons for this might be due to a high variety of largely uncharacterised competence inducers and a lack of understanding the ecological context of natural competence in cyanobacteria. To shed light on these questions, we describe what is known about the molecular mechanisms of natural competence in cyanobacteria and analyse how widespread this trait might be based on available genomic datasets. Potential regulators of natural competence and what benefits or drawbacks may derive from taking up foreign DNA are discussed. Overall, many unknowns about natural competence in cyanobacteria remain to be unravelled. A better understanding of underlying mechanisms and how to manipulate these, can aid the implementation of cyanobacteria as sustainable production chassis.

Natural transformation of the filamentous cyanobacterium Phormidium lacuna

Research for biotechnological applications of cyanobacteria focuses on synthetic pathways and bioreactor design, while little effort is devoted to introduce new, promising organisms in the field. Applications are most often based on recombinant work, and the establishment of transformation can be a risky, time-consuming procedure. In this work we demonstrate the natural transformation of the filamentous cyanobacterium Phormidium lacuna and insertion of a selection marker into the genome by homologous recombination. This is the first example for natural transformation filamentous non-heterocystous cyanobacterium. We found that Phormidium lacuna is polyploid, each cell has about 20-90 chromosomes. Transformed filaments were resistant against up to 14 mg/ml of kanamycin. Formerly, natural transformation in cyanobacteria has been considered a rare and exclusive feature of a few unicellular species. Our finding suggests that natural competence is more distributed among cyanobacteria than previously thought. This is supported by bioinformatic analyses which show that all protein factors for natural transformation are present in the majority of the analyzed cyanobacteria.

Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology

Recent advances in synthetic biology and an emerging algal biotechnology market have spurred a prolific increase in the availability of molecular tools for cyanobacterial research. Nevertheless, work to date has focused primarily on only a small subset of model species, which arguably limits fundamental discovery and applied research towards wider commercialisation. Here, we review the requirements for uptake of new strains, including several recently characterised fast-growing species and promising non-model species. Furthermore, we discuss the potential applications of new techniques available for transformation, genetic engineering and regulation, including an up-to-date appraisal of current Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein (CRISPR/Cas) and CRISPR interference (CRISPRi) research in cyanobacteria. We also provide an overview of several exciting molecular tools that could be ported to cyanobacteria for more advanced metabolic engineering approaches (e.g., genetic circuit design). Lastly, we introduce a forthcoming mutant library for the model species Synechocystis sp. PCC 6803 that promises to provide a further powerful resource for the cyanobacterial research community.

Genomics Approaches to Deciphering Natural Transformation in Cyanobacteria

Natural transformation is the process by which bacteria actively take up and maintain extracellular DNA. This naturally occurring process is widely used as a genetic modification method in bacterial species, and is crucial for the efficient genetic modification of organisms in an industrial setting. Cyanobacteria are oxygenic photosynthetic microbes that are promising platforms for bioproduction of fuels, chemicals, and feedstocks. Using CO₂ and sunlight alone, cyanobacteria can make these valuable bioproducts in a carbon-neutral manner. While genetic modifications have been performed in a number of cyanobacterial strains, natural transformation has been successfully demonstrated in only a handful of species. Even though thousands of cyanobacterial strains have been deposited in culture collections and hundreds of these species have had their genomes sequenced, only a few of these organisms have been experimentally transformed. Although there are many aspects of cyanobacterial biology that provide exciting opportunities for biological investigation, the absence of a rapid and straightforward genetic modification method such as natural transformation hinders research efforts to understand some of the fascinating nuances of cyanobacterial physiology. The ability to use natural transformation in more strains of cyanobacteria would facilitate the rapid employment of these organisms in bioproduction settings. This article discusses recent advances in the understanding of natural transformation in cyanobacteria. Additionally, it identifies gaps in the current knowledge about cyanobacterial natural transformation and provides an overview of how new genomic technologies may be implemented to understand this important process.

Thermosynechococcus as a thermophilic photosynthetic microbial cell factory for CO2 utilisation

Thermophilic unicellular cyanobacterium Thermosynechococcus elongatus PKUAC-SCTE542, has been developed as a thermophilic photosynthetic microbial cell factory for CO₂ utilisation. The strain exhibits its highest growth rate around 55 °C, can withstand up to 15% CO₂, and up to 0.5 M concentration of sodium bicarbonate. The strain is also capable of resisting a 200 ppm concentration of NO and SO₂ in simulated flue gasses, and these compounds have a positive effect on its growth. Whole genome sequencing of the strain revealed the presence of numerous forms of active transport of nutrients and additional chaperones acting as the predominant mechanism of strain adaptation to high temperatures. Based on the sequenced genome, two neutral gene insertion sites have been identified and engineered using modular vectors. Site-specific knock-ins and knock-outs have been performed using the spectinomycin resistance gene and proved functional, enabling future application of the strain to produce biofuels and biochemicals from waste CO₂.

Isoprenoid-Based Biofuels: Homologous Expression and Heterologous Expression in Prokaryotes

Enthusiasm for mining advanced biofuels from microbial hosts has increased remarkably in recent years. Isoprenoids are one of the highly diverse groups of secondary metabolites and are foreseen as an alternative to petroleum-based fuels. Most of the prokaryotes synthesize their isoprenoid backbone via the deoxyxylulose-5-phosphate pathway from glyceraldehyde-3-phosphate and pyruvate, whereas eukaryotes synthesize isoprenoids via the mevalonate pathway from acetyl coenzyme A (acetyl-CoA). Microorganisms do not accumulate isoprenoids in large quantities naturally, which restricts their application for fuel purposes. Various metabolic engineering efforts have been utilized to overcome the limitations associated with their natural and nonnatural production. The introduction of heterologous pathways/genes and overexpression of endogenous/homologous genes have shown a remarkable increase in isoprenoid yield and substrate utilization in microbial hosts. Such modifications in the hosts' genomes have enabled researchers to develop commercially competent microbial strains for isoprenoid-based biofuel production utilizing a vast array of substrates. The present minireview briefly discusses the recent advancement in metabolic engineering efforts in prokaryotic hosts for the production of isoprenoid-based biofuels, with an emphasis on endogenous, homologous, and heterologous expression strategies.

Premethylation of foreign DNA improves integrative transformation efficiency in Synechocystis sp. strain PCC 6803

Restriction digestion of foreign DNA is one of the key biological barriers against genetic transformation in microorganisms. To establish a high-efficiency transformation protocol in the model cyanobacterium, Synechocystis sp. strain PCC 6803 (Synechocystis 6803), we investigated the effects of premethylation of foreign DNA on the integrative transformation of this strain. In this study, two type II methyltransferase-encoding genes, i.e., sll0729 (gene M) and slr0214 (gene C), were cloned from the chromosome of Synechocystis 6803 and expressed in Escherichia coli harboring an integration plasmid. After premethylation treatment in E. coli, the integration plasmid was extracted and used for transformation of Synechocystis 6803. The results showed that although expression of methyltransferase M had little impact on the transformation of Synechocystis 6803, expression of methyltransferase C resulted in 11- to 161-fold-higher efficiency in the subsequent integrative transformation of Synechocystis 6803. Effective expression of methyltransferase C, which could be achieved by optimizing the 5' untranslated region, was critical to efficient premethylation of the donor DNA and thus high transformation efficiency in Synechocystis 6803. Since premethylating foreign DNA prior to transforming Synechocystis avoids changing the host genetic background, the study thus provides an improved method for high-efficiency integrative transformation of Synechocystis 6803.

Metabolic engineering for isoprenoid-based biofuel production

Sustainable economic and industrial growth is the need of the hour and it requires renewable energy resources having better performance and compatibility with existing fuel infrastructure from biological routes. Isoprenoids (C ≥ 5) can be a potential alternative due to their diverse nature and physiochemical properties similar to that of petroleum based fuels. In the past decade, extensive research has been done to utilize metabolic engineering strategies in micro-organisms primarily, (i) to overcome the limitations associated with their natural and non-natural production and (ii) to develop commercially competent microbial strain for isoprenoid-based biofuel production. This review briefly describes the engineered isoprenoid biosynthetic pathways in well-characterized microbial systems for the production of several isoprenoid-based biofuels and fuel precursors.

Molecular interactions between photosystem I and ferredoxin: an integrated energy frustration and experimental model

The stromal domain (PsaC, PsaD, and PsaE) of photosystem I (PSI) reduces transiently bound ferredoxin (Fd) or flavodoxin. Experimental structures exist for all of these protein partners individually, but no experimental structure of the PSI/Fd or PSI/flavodoxin complexes is presently available. Molecular models of Fd docked onto the stromal domain of the cyanobacterial PSI site are constructed here utilizing X-ray and NMR structures of PSI and Fd, respectively. Predictions of potential protein-protein interaction regions are based on experimental site-directed mutagenesis and cross-linking studies to guide rigid body docking calculations of Fd into PSI, complemented by energy landscape theory to bring together regions of high energetic frustration on each of the interacting proteins. The results identify two regions of high localized frustration on the surface of Fd that contain negatively charged Asp and Glu residues. This study predicts that these regions interact predominantly with regions of high localized frustration on the PsaC, PsaD, and PsaE chains of PSI, which include several residues predicted by previous experimental studies.

Cyanobacteria as a Platform for Biofuel Production

Cyanobacteria have great potential as a platform for biofuel production because of their fast growth, ability to fix carbon dioxide gas, and their genetic tractability. Furthermore they do not require fermentable sugars or arable land for growth and so competition with cropland would be greatly reduced. In this perspective we discuss the challenges and areas for improvement most pertinent for advancing cyanobacterial fuel production, including: improving genetic parts, carbon fixation, metabolic flux, nutrient requirements on a large scale, and photosynthetic efficiency using natural light.

How hyperthermophiles adapt to change their lives: DNA exchange in extreme conditions

Transfer of DNA has been shown to be involved in genome evolution. In particular with respect to the adaptation of bacterial species to high temperatures, DNA transfer between the domains of bacteria and archaea seems to have played a major role. In addition, DNA exchange between similar species likely plays a role in repair of DNA via homologous recombination, a process that is crucial under DNA damaging conditions such as high temperatures. Several mechanisms for the transfer of DNA have been described in prokaryotes, emphasizing its general importance. However, until recently, not much was known about this process in prokaryotes growing in highly thermophilic environments. This review describes the different mechanisms of DNA transfer in hyperthermophiles, and how this may contribute to the survival and adaptation of hyperthermophilic archaea and bacteria to extreme environments.

Role of polyphosphate in thermophilic Synechococcus sp. from microbial mats

Synechococcus OS-B', a thermophilic unicellular cyanobacterium, recently isolated from the microbial mats in Octopus Spring (Yellowstone National Park), induces a suite of genes, including phosphatases and transporters, in response to phosphorus (P) starvation. Here we describe two different approaches to examine the ability of Synechococcus OS-B' to synthesize and break down polyphosphate (poly P), a key storage compound in many prokaryotes. First, we developed a transformation protocol to create mutants in the polyphosphate kinase (ppk), the major enzyme responsible for the synthesis of poly P. The ppk mutant exhibited a pleiotropic phenotype with defects in poly P accumulation, aberrant levels of Pho regulon transcripts, growth defects, and changes in cell size and exopolysaccharide levels, among others. Second, we measured transcripts of ppk and ppx (encoding the polyphosphatase) directly from mat samples and found that the levels varied dramatically over a diel cycle. We also used Western blot analysis to quantify levels of PPK and PPX and found that these enzymes differentially accumulated during the diel cycle. Levels of polyphosphate kinase peaked at night, while polyphosphatase levels were highest during the early morning hours. We hypothesize that the opposing activities of these two enzymes allow cells to store and utilize poly P to optimize growth over a diel cycle.

Thermodynamic characterization of a thermostable antibiotic resistance enzyme, the aminoglycoside nucleotidyltransferase (4')

The aminoglycoside nucleotidyltransferase (4') (ANT) is an aminoglycoside-modifying enzyme that detoxifies antibiotics by nucleotidylating at the C4'-OH site. Previous crystallographic studies show that the enzyme is a homodimer and each subunit binds one kanamycin and one Mg-AMPCPP, where the transfer of the nucleotidyl group occurs between the substrates bound to different subunits. In this work, sedimentation velocity analysis of ANT by analytical ultracentrifugation showed the enzyme exists as a mixture of a monomer and a dimer in solution and that dimer formation is driven by hydrophobic interactions between the subunits. The binding of aminoglycosides shifts the equilibrium toward dimer formation, while the binding of the cosubstrate, Mg-ATP, has no effect on the monomer-dimer equilibrium. Surprisingly, binding of several divalent cations, including Mg(2+), Mn(2+), and Ca(2+), to the enzyme also shifted the equilibrium in favor of dimer formation. Binding studies, performed by electron paramagnetic resonance spectroscopy, showed that divalent cations bind to the aminoglycoside binding site in the absence of substrates with a stoichiometry of 2:1. Energetic aspects of binding of all aminoglycosides to ANT were determined by isothermal titration calorimetry to be enthalpically favored and entropically disfavored with an overall favorable Gibbs energy. Aminoglycosides in the neomycin class each bind to the enzyme with significantly different enthalpic and entropic contributions, while those of the kanamycin class bind with similar thermodynamic parameters.

Transformation and conjugal transfer of foreign genes into the filamentous multicellular cyanobacteria (subsection V) Fischerella and Chlorogloeopsis

Cyanobacteria of subsection V grow as filaments with asymmetrical cell divisions that can generate a true-branching phenotype. Members of the genera Fischerella and Chlorogloeopsis furthermore differentiate akinetes (spore-like resting stages), heterocysts (specialized in nitrogen fixation) and hormogonia (cell aggregates with gliding motility for colonization and dispersal). Genetic approaches to studying the complex morphology and differentiations of these prokaryotes require transformation techniques. For Fischerella and Chlorogloeopsis reliable protocols for introducing foreign genes are lacking. Here, we explored conjugation, electroporation, and biolistic DNA transfer methods in Fischerella and Chlorogloeopsis, using the cyanobacterial replicon pRL25C as a marker. We successfully transformed Fischerella muscicola PCC 7414 and Chlorogloeopsis fritschii PCC 6912 and were able to express the GFP reporter protein under two different promoters: the nitrogen regulated (p) glnA and the strong E. coli hybrid (p) trc. For Fischerella all methods worked, for Chlorogloeopsis electroporation was unsuccessful. For both strains conjugation delivered the most reproducible results, whereby partial removal of the exopolysaccharide sheath by salt washing was a critical step.

Synthetic biology in cyanobacteria engineering and analyzing novel functions

Cyanobacteria are the only prokaryotes capable of using sunlight as their energy, water as an electron donor, and air as a source of carbon and, for some nitrogen-fixing strains, nitrogen. Compared to algae and plants, cyanobacteria are much easier to genetically engineer, and many of the standard biological parts available for Synthetic Biology applications in Escherichia coli can also be used in cyanobacteria. However, characterization of such parts in cyanobacteria reveals differences in performance when compared to E. coli, emphasizing the importance of detailed characterization in the cellular context of a biological chassis. Furthermore, cyanobacteria possess special characteristics (e.g., multiple copies of their chromosomes, high content of photosynthetically active proteins in the thylakoids, the presence of exopolysaccharides and extracellular glycolipids, and the existence of a circadian rhythm) that have to be taken into account when genetically engineering them. With this chapter, the synthetic biologist is given an overview of existing biological parts, tools and protocols for the genetic engineering, and molecular analysis of cyanobacteria for Synthetic Biology applications.

Horizontal gene transfer in cyanobacterial signature genes

Comparison of 15 phylogenetically diverse cyanobacterial genomes identified an updated list of 183 signature genes that are widely found in cyanobacteria but absent in non-cyanobacterial species. These signature genes comprise the unique portion of the core cyanobacterial phenotype, and their absence from other lineages implies that if they arose by horizontal gene transfer (HGT), it likely occurred before the last shared cyanobacterial ancestor. A remaining issue is whether or not these signature genes would be relatively immune to HGT within the cyanobacterial lineage. Phylogenetic trees for each signature gene were constructed and compared to cyanobacterial groupings based on 16S rRNA sequences, with clear incongruence considered indicative of HGT. Approximately 18% of the signature genes exhibited such anomalies, indicating that the incidence of inter-lineage HGT has been significant. A preliminary analysis of intra-lineage transfer was conducted using four Synechococcus/Prochlorococcus species. In this case, it was found that 13% of the signature genes had likely been involved in within group HGT. In order to compare this level of likely HGT to other gene types, the analysis was extended to 1380 genes shared by the four Synechococcus/Prochlorococcus species. Successful HGT events appear to be most frequent among genes involved in photosynthesis/respiration and genes of unknown function, many of which are signature genes. This is consistent with the hypothesis that genes that most directly effect competition and adaptation of similar species in neighboring niches would be most usefully transferred. Such genes may be more easily integrated into a new genomic environment due to close similarities in regulatory circuits. In summary, signature genes are not immune from HGT and in fact may be favored candidates for HGT among closely related cyanobacterial strains.

2,2'-beta-hydroxylase (CrtG) is involved in carotenogenesis of both nostoxanthin and 2-hydroxymyxol 2'-fucoside in Thermosynechococcus elongatus strain BP-1

We identified the molecular structures, including the stereochemistry, of all carotenoids in Thermosynechococcus elongatus strain BP-1. The major carotenoid was beta-carotene, and its hydroxyl derivatives of (3R)-beta-cryptoxanthin, (3R,3'R)-zeaxanthin, (2R,3R,3'R)-caloxanthin and (2R,3R,2'R,3'R)-nostoxanthin were also identified. The myxol glycosides were identified as (3R,2'S)-myxol 2'-fucoside and (2R,3R,2'S)-2-hydroxymyxol 2'-fucoside. 2-Hydroxymyxol 2'-fucoside is a novel carotenoid, and similar carotenoids of 4-hydroxymyxol glycosides were previously named aphanizophyll. Ketocarotenoids, such as echinenone and 4-ketomyxol, which are unique carotenoids in cyanobacteria, were absent, and genes coding for both beta-carotene ketolases, crtO and crtW, were absent in the genome. From a homology search, the Tlr1917 amino acid sequence was found to be 41% identical to 2,2'- beta-hydroxylase (CrtG) from Brevundimonas sp. SD212, which produces nostoxanthin from zeaxanthin. In the crtG disruptant mutant, 2-hydroxymyxol 2'-fucoside, caloxanthin and nostoxanthin were absent, and the levels of both myxol 2'-fucoside and zeaxanthin were higher. Therefore, the gene has a CrtG function for both myxol to 2-hydroxymyxol and zeaxanthin to nostoxanthin. This is the first functional identification of CrtG in cyanobacteria. We also investigated the distribution of crtG-like genes, and 2-hydroxymyxol and/or nostoxanthin, in cyanobacteria. Based on the identification of the carotenoids and the completion of the entire nucleotide sequence of the genome in T. elongatus, we propose a biosynthetic pathway of the carotenoids and the corresponding genes and enzymes.

Natural genetic transformation: prevalence, mechanisms and function

Studies show that gene acquisition through natural transformation has contributed significantly to the adaptation and ecological diversification of several bacterial species. Relatively little is still known, however, about the prevalence and phylogenetic distribution of organisms possessing this property. Thus, whether natural transformation only benefits a limited number of species or has a large impact on lateral gene flow in nature remains a matter of speculation. Here we will review the most recent advances in our understanding of the phenomenon and discuss its possible biological functions.

Higher plant chloroplasts import the mRNA coding for the eucaryotic translation initiation factor 4E

Plant chloroplasts probably originate from an endosymbiosis event between a photosynthetic bacteria and a eucaryotic cell. The proper functioning of this association requires a high level of integration between the chloroplastic genome and the plant cell genome. Many chloroplastic genes have been transferred to the nucleus of the host cell and the proteins coded by these genes are imported into the chloroplast. Chloroplastic activity also regulates the expression of these genes at the transcriptional and post-transcriptional levels. The importation of nucleic acids from the host cell into the chloroplast has never been observed. This work show that the mRNA coding for the eucaryotic translation factor 4E, an essential regulator of translation, enters the chloroplast in four different plant species, and is located in the stroma. Furthermore, the localization in the chloroplast of an heterologous GFP mRNA fused to the eIF4E RNA was also observed.

Stable transformation of Chromobacterium violaceum with a broad-host-range plasmid

Stable transformants of Chromobacterium violaceum were obtained by high-voltage electroporation with a 7-kilobase binary plasmid. The technique was reliable, reproducible, and simple, with efficiencies of 10(5) transformants/microg of plasmid DNA. The electrical conditions that resulted in the highest efficiencies were short pulse length (4.4-4.5 ms) and high voltage (12.5 kV/cm). The numbers of transformants were almost the same during the growth exponential phase (variation at optical density) and resulted in the highest efficiencies at DNA concentration of 250 pg/ml. Saturation appeared to begin at 4 microg/ml of DNA. This method of C. violaceum transformation should enhance the genetic and biotechnological research by providing a valuable, widely used procedure of introducing DNA into this bacterium.

Functionally important substructures of circadian clock protein KaiB in a unique tetramer complex

KaiB is a component of the circadian clock molecular machinery in cyanobacteria, which are the simplest organisms that exhibit circadian rhythms. Here we report the x-ray crystal structure of KaiB from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. The KaiB crystal diffracts at a resolution of 2.6 A and includes four subunits organized as a dimer of dimers, each composed of two non-equivalent subunits. The overall shape of the tetramer is an elongated hexagonal plate, with a single positively charged cleft flanked by two negatively charged ridges whose surfaces includes several terminal chains. Site-directed mutagenesis of Synechococcus KaiB confirmed that alanine substitution of residues Lys-11 or Lys-43 in the cleft, or deletion of C-terminal residues 95-108, which forms part of the ridges, strongly weakens in vivo circadian rhythms. Characteristics of KaiB deduced from the x-ray crystal structure were also confirmed by physicochemical measurements of KaiB in solution. These data suggest that the positively charged cleft and flanking negatively charged ridges in KaiB are essential for the biological function of KaiB in the circadian molecular machinery in cyanobacteria.

Construction of unmodified oligonucleotide-based microarrays in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1: screening of the candidates for circadianly expressed genes

DNA microarrays with unmodified oligonucleotide probes are a cost-effective and high-performance alternative to cDNA microarrays. We searched every gene in the genome of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 for 45-mer oligonucleotide probes with optimal nucleotide sequences, and found such probes in 90% of the genes. Using the probes, we constructed a microarray that represented 2,397 genes (95% of total genes). We detected only low signals in the negative control probes whose nucleotide sequences are not contained in the T. elongatus genome, demonstrating that specific hybridization occurred. To evaluate the reliability of the measurements obtained by the oligonucleotide microarray, we performed microarray experiments using RNA samples from two different time points of circadianly synchronized cultures, LL2 (early sub-jective day) and LL14 (early subjective night). Measurements obtained from the two independent microarray hybridizations were highly concordant (correlation coefficient [r] > 0.8). Northern blot analyses of 20 genes confirmed that expression changes detected by the microarrays were correct (r = 0.832). We identified 143 candidate clock-controlled genes whose expression levels at LL2 and LL14 were significantly different. Expression of 69 of them was enhanced at LL14 while expression of the other 74 was enhanced at LL2. The physiological functions of the genes were diverse and included metabolism, translation, transcription, membrane transport, DNA replication and repair, and cell growth and death.

Circadian rhythms in the thermophilic cyanobacterium Thermosynechococcus elongatus: compensation of period length over a wide temperature range

Proteins derived from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, which performs plant-type oxygenic photosynthesis, are suitable for biochemical, biophysical, and X-ray crystallographic studies. We developed an automated bioluminescence real-time monitoring system for the circadian clock in the thermophilic cyanobacterium T. elongatus BP-1 that uses a bacterial luciferase gene set (Xl luxAB) derived from Xenorhabdus luminescens as a bioluminescence reporter gene. A promoter region of the psbA1 gene of T. elongatus was fused to the Xl luxAB gene set and inserted into a specific targeting site in the genome of T. elongatus. The bioluminescence from the cells of the psbA1-reporting strain was measured by an automated monitoring apparatus with photomultiplier tubes. The strain exhibited the circadian rhythms of bioluminescence with a 25-h period length for at least 10 days in constant light and temperature. The rhythms were reset by light-dark cycle, and their period length was almost constant over a wide range of temperatures (30 to 60 degrees C). Theses results indicate that T. elongatus has the circadian clock that is widely temperature compensated.

Crystal structure of the C-terminal clock-oscillator domain of the cyanobacterial KaiA protein

KaiA, KaiB and KaiC constitute the circadian clock machinery in cyanobacteria, and KaiA activates kaiBC expression whereas KaiC represses it. Here we show that KaiA is composed of three functional domains, the N-terminal amplitude-amplifier domain, the central period-adjuster domain and the C-terminal clock-oscillator domain. The C-terminal domain is responsible for dimer formation, binding to KaiC, enhancing KaiC phosphorylation and generating the circadian oscillations. The X-ray crystal structure at a resolution of 1.8 A of the C-terminal clock-oscillator domain of KaiA from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 shows that residue His270, located at the center of a KaiA dimer concavity, is essential to KaiA function. KaiA binding to KaiC probably occurs via the concave surface. On the basis of the structure, we predict the structural roles of the residues that affect circadian oscillations.