Improved Genetic Transformation of the Thermophilic Cyanobacterium, Thermosynechococcus elongatus BP-1

A toolbox to engineer the highly productive cyanobacterium Synechococcus sp. PCC 11901

Synechococcus sp. PCC 11901 (PCC 11901) is a fast-growing marine cyanobacterial strain that has a capacity for sustained biomass accumulation to very high cell densities, comparable to that achieved by commercially relevant heterotrophic organisms. However, genetic tools to engineer PCC 11901 for biotechnology applications are limited. Here we describe a suite of tools based on the CyanoGate MoClo system to unlock the engineering potential of PCC 11901. First, we characterized neutral sites suitable for stable genomic integration that do not affect growth even at high cell densities. Second, we tested a suite of constitutive promoters, terminators, and inducible promoters including a 2,4-diacetylphloroglucinol (DAPG)-inducible PhlF repressor system, which has not previously been demonstrated in cyanobacteria and showed tight regulation and a 228-fold dynamic range of induction. Lastly, we developed a DAPG-inducible dCas9-based CRISPR interference (CRISPRi) system and a modular method to generate markerless mutants using CRISPR-Cas12a. Based on our findings, PCC 11901 is highly responsive to CRISPRi-based repression and showed high efficiencies for single insertion (31% to 81%) and multiplex double insertion (25%) genome editing with Cas12a. We envision that these tools will lay the foundations for the adoption of PCC 11901 as a robust model strain for engineering biology and green biotechnology.

Coaggregation Occurs between a Piliated Unicellular Cyanobacterium, Thermosynechococcus, and a Filamentous Bacterium, Chloroflexus aggregans

Cyanobacteria are widely distributed in natural environments including geothermal areas. A unicellular cyanobacterium, Thermosynechococcus, in a deeply branching lineage, develops thick microbial mats with other bacteria, such as filamentous anoxygenic photosynthetic bacteria in the genus Chloroflexus, in slightly alkaline hot-spring water at ~55 °C. However, Thermosynechococcus strains do not form cell aggregates under axenic conditions, and the cells are dispersed well in the culture. In this study, Thermosynechococcus sp. NK55a and Chloroflexus aggregans NBF, isolated from Nakabusa Hot Springs (Nagano, Japan), were mixed in an inorganic medium and incubated at 50 °C under incandescent light. Small cell aggregates were detected after 4 h incubation, the size of cell aggregates increased, and densely packed cell aggregates (100-200 µm in diameter) developed. Scanning electron microscopy analysis of cell aggregates found that C. aggregans filaments were connected with Thermosynechococcus sp. cells via pili-like fibers. Co-cultivation of C. aggregans with a pili-less mutant of Thermosynechococcus sp. did not form tight cell aggregates. Cell aggregate formation was observed under illumination with 740 nm LED, which was utilized only by C. aggregans. These results suggested that Chloroflexus filaments gather together via gliding motility, and piliated cyanobacterial cells cross-link filamentous cells to form densely packed cell aggregates.

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.

Isolation of a novel heterodimeric PSII complex via strep-tagged PsbO

The multi-subunit membrane protein complex photosystem II (PSII) catalyzes the light-driven oxidation of water and with this the initial step of photosynthetic electron transport in plants, algae, and cyanobacteria. Its biogenesis is coordinated by a network of auxiliary proteins that facilitate the stepwise assembly of individual subunits and cofactors, forming various intermediate complexes until fully functional mature PSII is present at the end of the process. In the current study, we purified PSII complexes from a mutant line of the thermophilic cyanobacterium Thermosynechococcus vestitus BP-1 in which the extrinsic subunit PsbO, characteristic for active PSII, was fused with an N-terminal Twin-Strep-tag. Three distinct PSII complexes were separated by ion-exchange chromatography after the initial affinity purification. Two complexes differ in their oligomeric state (monomeric and dimeric) but share the typical subunit composition of mature PSII. They are characterized by the very high oxygen evolving activity of approx. 6000 μmol O₂·(mg Chl·h)^-1. Analysis of the third (heterodimeric) PSII complex revealed lower oxygen evolving activity of approx. 3000 μmol O₂·(mg Chl·h)^-1 and a manganese content of 2.7 (±0.2) per reaction center compared to 3.7 (±0.2) of fully active PSII. Mass spectrometry and time-resolved fluorescence spectroscopy further indicated that PsbO is partially replaced by Psb27 in this PSII fraction, thus implying a role of this complex in PSII repair.

Generation of miniploid cells and improved natural transformation procedure for a model cyanobacterium Synechococcus elongatus PCC 7942

The biotechnologically important and naturally transformable cyanobacterium, Synechococcus elongatus PCC 7942, possesses multiple genome copies irrespective of its growth rate or condition. Hence, segregating mutations across all genome copies typically takes several weeks. In this study, Synechococcus 7942 cultivation on a solid growth medium was optimised using different concentrations of agar, the addition of antioxidants, and overexpression of the catalase gene to facilitate the rapid acquisition of colonies and fully segregated lines. Synechococcus 7942 was grown at different temperatures and nutritional conditions. The miniploid cells were identified using flow cytometry and fluorimetry. The natural transformation was carried out using miniploid cells and validated with PCR and high performance liquid chromatography (HPLC). We identified that 0.35% agar concentration and 200 IU of catalase could improve the growth of Synechococcus 7942 on a solid growth medium. Furthermore, overexpression of a catalase gene enhanced the growth rate and supported diluted culture to grow on a solid medium. Our results reveal that high temperature and phosphate-depleted cells contain the lowest genome copies (2.4 ± 0.3 and 1.9 ± 0.2) and showed the potential to rapidly produce fully segregated mutants. In addition, higher antibiotic concentrations improve the selection of homozygous transformants while maintaining similar genome copies at a constant temperature. Based on our observation, we have an improved cultivation and natural transformation protocol for Synechococcus 7942 by optimising solid media culturing, generating low-ploidy cells that ultimately reduced the time required for the complete segregation of engineered lines.

Thermosynechococcus switches the direction of phototaxis by a c-di-GMP-dependent process with high spatial resolution

Many cyanobacteria, which use light as an energy source via photosynthesis, show directional movement towards or away from a light source. However, the molecular and cell biological mechanisms for switching the direction of movement remain unclear. Here, we visualized type IV pilus-dependent cell movement in the rod-shaped thermophilic cyanobacterium Thermosynechococcus vulcanus using optical microscopy at physiological temperature and light conditions. Positive and negative phototaxis were controlled on a short time scale of 1 min. The cells smoothly moved over solid surfaces towards green light, but the direction was switched to backward movement when we applied additional blue light illumination. The switching was mediated by three photoreceptors, SesA, SesB, and SesC, which have cyanobacteriochrome photosensory domains and synthesis/degradation activity of the bacterial second messenger cyclic dimeric GMP (c-di-GMP). Our results suggest that the decision-making process for directional switching in phototaxis involves light-dependent changes in the cellular concentration of c-di-GMP. Direct visualization of type IV pilus filaments revealed that rod-shaped cells can move perpendicular to the light vector, indicating that the polarity can be controlled not only by pole-to-pole regulation but also within-a-pole regulation. This study provides insights into previously undescribed rapid bacterial polarity regulation via second messenger signalling with high spatial resolution.

Structural insights into a dimeric Psb27-photosystem II complex from a cyanobacterium Thermosynechococcus vulcanus

Photosystem II (PSII) is a multisubunit pigment-protein complex and catalyzes light-driven water oxidation, leading to the conversion of light energy into chemical energy and the release of molecular oxygen. Psb27 is a small thylakoid lumen-localized protein known to serve as an assembly factor for the biogenesis and repair of the PSII complex. The exact location and binding fashion of Psb27 in the intermediate PSII remain elusive. Here, we report the structure of a dimeric Psb27-PSII complex purified from a psbV deletion mutant (ΔPsbV) of the cyanobacterium Thermosynechococcus vulcanus, solved by cryo-electron microscopy. Our structure showed that Psb27 is associated with CP43 at the luminal side, with specific interactions formed between Helix 2 and Helix 3 of Psb27 and a loop region between Helix 3 and Helix 4 of CP43 (loop C) as well as the large, lumen-exposed and hydrophilic E-loop of CP43. The binding of Psb27 imposes some conflicts with the N-terminal region of PsbO and also induces some conformational changes in CP43, CP47, and D2. This makes PsbO unable to bind in the Psb27-PSII. Conformational changes also occurred in D1, PsbE, PsbF, and PsbZ; this, together with the conformational changes occurred in CP43, CP47, and D2, may prevent the binding of PsbU and induce dissociation of PsbJ. This structural information provides important insights into the regulation mechanism of Psb27 in the biogenesis and repair of PSII.

Structural insights into photosystem II assembly

Biogenesis of photosystem II (PSII), nature's water-splitting catalyst, is assisted by auxiliary proteins that form transient complexes with PSII components to facilitate stepwise assembly events. Using cryo-electron microscopy, we solved the structure of such a PSII assembly intermediate from Thermosynechococcus elongatus at 2.94 Å resolution. It contains three assembly factors (Psb27, Psb28 and Psb34) and provides detailed insights into their molecular function. Binding of Psb28 induces large conformational changes at the PSII acceptor side, which distort the binding pocket of the mobile quinone (Q_B) and replace the bicarbonate ligand of non-haem iron with glutamate, a structural motif found in reaction centres of non-oxygenic photosynthetic bacteria. These results reveal mechanisms that protect PSII from damage during biogenesis until water splitting is activated. Our structure further demonstrates how the PSII active site is prepared for the incorporation of the Mn₄CaO₅ cluster, which performs the unique water-splitting reaction.

Aqueous-soluble bipyridine cobalt(ii/iii) complexes act as direct redox mediators in photosystem I-based biophotovoltaic devices

Sustainable energy production is critical for meeting growing worldwide energy demands. Due to its stability and reduction potential, photosystem I (PSI) is attractive as the photosensitizer in biophotovoltaic devices. Herein, we characterize aqueous and organic solvent soluble synthetic bipyridine-based cobalt complexes as redox mediators for PSI-based biophotovoltaics applications. Cobalt-based complexes are not destructive to protein and have appropriate midpoint potentials for electron donation to PSI. We report on PSI stability in organic solvents commonly used in biophotovoltaics. We also show the effects of a mixed organic solvent phase on PSI reduction kinetics, slowing reduction rates approximately 8–38 fold as compared to fully aqueous systems, with implications for dye regeneration rates in PSI-based biophotovoltaics. Further, we show evidence of direct electron transfer from cobalt complexes to PSI. Finally, we report on photocurrent generation from Co mediator-PSI biophotovoltaic devices. Taken together, we discuss the development of novel Co complexes and our ability to fine-tune their characteristics via functional groups and counteranion choice to drive interaction with a biological electron acceptor on multiple levels from redox midpoints, spectral overlap, and solvent requirements, among others. This work suggests that fine-tuning of redox active species for interaction with a biological partner is possible for the creation and improvement of low cost, carbon-neutral energy production in the future.

Sustainable energy production is critical for meeting growing worldwide energy demands.

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.

The Role of the Cyanobacterial Type IV Pilus Machinery in Finding and Maintaining a Favourable Environment

Type IV pili (T4P) are proteinaceous filaments found on the cell surface of many prokaryotic organisms and convey twitching motility through their extension/retraction cycles, moving cells across surfaces. In cyanobacteria, twitching motility is the sole mode of motility properly characterised to date and is the means by which cells perform phototaxis, the movement towards and away from directional light sources. The wavelength and intensity of the light source determine the direction of movement and, sometimes in concert with nutrient conditions, act as signals for some cyanobacteria to form mucoid multicellular assemblages. Formation of such aggregates or flocs represents an acclimation strategy to unfavourable environmental conditions and stresses, such as harmful light conditions or predation. T4P are also involved in natural transformation by exogenous DNA, secretion processes, and in cellular adaptation and survival strategies, further cementing the role of cell surface appendages. In this way, cyanobacteria are finely tuned by external stimuli to either escape unfavourable environmental conditions via phototaxis, exchange genetic material, and to modify their surroundings to fit their needs by forming multicellular assemblies.

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.

Co-crystal Structure of Thermosynechococcus elongatus Sucrose Phosphate Synthase With UDP and Sucrose-6-Phosphate Provides Insight Into Its Mechanism of Action Involving an Oxocarbenium Ion and the Glycosidic Bond

In green species, sucrose can help antagonize abiotic stress. Sucrose phosphate synthase (SPS) is a well-known rate-limiting enzyme in the synthesis of sucrose. To date, however, there is no known crystal structure of SPS from plant or cyanobacteria. In this study, we report the first co-crystal structure of SPS from Thermosynechococcus elongatus with UDP and sucrose-6-phosphate (S6P). Within the catalytic site, the side chains of His158 and Glu331, along with two phosphate groups from UDP, form hydrogen bonds with the four hydroxyl groups of the glucose moiety in S6P. This association causes these four hydroxyl groups to become partially negatively charged, thus promoting formation of the C1 oxocarbenium ion. Breakage of the hydrogen bond between His158 and one of the hydroxyl groups may trigger covalent bond formation between the C1 oxocarbenium ion and the C2 hydroxyl of fructose-6-phosphate. Consistent with our structural model, we observed that two SPS mutants, H158A and E331A, lost all catalytic activity. Moreover, electron density of residues from two loops (loop1 and loop2) in the SPS A-domain was not observed, suggest their dynamic nature. B-factor analysis and molecular dynamics stimulations of the full-length enzyme and A-domain indicate that both loops are crucial for binding and release of substrate and product. In addition, temperature gradient analysis shows that SPS exhibits its highest activity at 70°C, suggesting that this enzyme has the potential of being used in industrial production of S6P.

Comparative Genomic Analysis of a Novel Strain of Taiwan Hot-Spring Cyanobacterium Thermosynechococcus sp. CL-1

Thermosynechococcus is a genus of thermophilic unicellular cyanobacteria that are dominant in microbial mats at about 50–65°C in alkaline hot springs of eastern Asia. We used PacBio SMRT Sequencing to sequence the complete genome of a novel strain of thermophilic cyanobacterium, Thermosynechococcus sp. CL-1, isolated from the Chin-Lun hot spring (pH 9.3, 62°C) in Taiwan. Genome-scale phylogenetic analysis and average nucleotide identity (ANI) results suggested that CL-1 is a new species in the genus Thermosynechococcus. Comparative genome analysis revealed divergent genome structures of Thermosynechococcus strains. In addition, the distinct genetic differences between CL-1 and the other Thermosynechococcus strains are related to photosynthesis, transporters, signal transduction, the chaperone/usher system, nitric oxide protection, antibiotic resistance, prokaryotic immunity systems, and other physiological processes. This study suggests that Thermosynechococcus strains have actively acquired many putative horizontally transferred genes from other bacteria that enabled them to adapt to different ecological niches and stressful conditions in hot springs.

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.

Transport of organic substances through the cytoplasmic membrane of cyanobacteria

Cyanobacteria are mainly known to incorporate inorganic molecules like carbon dioxide and ammonia from the environment into organic material within the cell. Nevertheless cyanobacteria do import and export organic substances through the cytoplasmic membrane and these processes are essential for all cyanobacteria. In addition understanding the mechanisms of transport of organic molecules through the cytoplasmic membrane might become very important. Genetically modified strains of cyanobacteria could serve as producers and exporters of commercially important substances. In this review we attempt to present all data of transport of organic molecules through the cytoplasmic membrane of cyanobacteria that are currently available with the transported molecules ordered according to their chemical classes.

Species-specific transcriptomic network inference of interspecies interactions

The advent of high-throughput 'omics approaches coupled with computational analyses to reconstruct individual genomes from metagenomes provides a basis for species-resolved functional studies. Here, a mutual information approach was applied to build a gene association network of a commensal consortium, in which a unicellular cyanobacterium Thermosynechococcus elongatus BP1 supported the heterotrophic growth of Meiothermus ruber strain A. Specifically, we used the context likelihood of relatedness (CLR) algorithm to generate a gene association network from 25 transcriptomic datasets representing distinct growth conditions. The resulting interspecies network revealed a number of linkages between genes in each species. While many of the linkages were supported by the existing knowledge of phototroph-heterotroph interactions and the metabolism of these two species several new interactions were inferred as well. These include linkages between amino acid synthesis and uptake genes, as well as carbohydrate and vitamin metabolism, terpenoid metabolism and cell adhesion genes. Further topological examination and functional analysis of specific gene associations suggested that the interactions are likely to center around the exchange of energetically costly metabolites between T. elongatus and M. ruber. Both the approach and conclusions derived from this work are widely applicable to microbial communities for identification of the interactions between species and characterization of community functioning as a whole.

Development and optimization of genetic toolboxes for a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

The fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 (hereafter Synechococcus 2973) has been considered a good chassis candidate for "microbial cell factory" as it can perform oxygenic photosynthesis and its doubling time can be as short as 1.9 h. However, the limited genetic tools currently restrict its further research and application efforts using synthetic biology approaches. In this study, a series of genetic tools were systematically developed and optimized for Synechococcus 2973. First, the introduction of Tfp pilus assembly protein encoding gene pilN into Synechococcus 2973 successfully recovered its natural transformability, which greatly simplified the DNA transformation process. Second, a series of promoters with different strengths were evaluated and the super-strong promoters including P_cpc560 from Synechocystis sp. PCC 6803, native P_psbA2 and P_psbA3 of Synechococcus 2973 were found with the highest activity of β-galactosidase among those evaluated by miller values. Some promoters related to photosystems (i.e., P_psbA2, P_psbA3, P_6803psbA2 and P_cpc560) were also demonstrated to be induced by high intensity of light. Third, three lactose induction systems were evaluated, among which P_lac combined with lacI^q showed the best application prospect with great induction capacity, low leakage and middle induced expression. Fourth, the translational on riboswitch theoE* , the transcriptional off riboswitches theo/yitJ and xpt(C74U)/metE and an artificial inducing system combining theoE* with T7 RNA polymerase were successfully developed and characterized in Synechococcus 2973. Finally, by using T7 induction system to control the expression of both small RNA and chaperone Hfq, a small RNA regulatory tool was developed and optimized to be a strictly inducible off system for gene regulation in Synechococcus 2973. The work here presented valuable genetic toolboxes necessary for metabolic engineering and synthetic biology research in Synechococcus 2973, which will facilitate the future application of the fast growing cyanobacterial chassis.

Genetic identification of factors for extracellular cellulose accumulation in the thermophilic cyanobacterium Thermosynechococcus vulcanus: proposal of a novel tripartite secretion system

Cells of the thermophilic cyanobacterium Thermosynechococcus vulcanus strain RKN (NIES-2134) aggregate and produce extracellular cellulose under induced conditions of blue light and low temperature, and both aggregation and cellulose production require the cellulose synthase Tll0007 (XcsA) and photosensory diguanylate cyclases. However, overexpression of both the cellulose synthase and a constitutively active diguanylate cyclase was not sufficient to induce cellulose-mediated cell aggregation under normal growth conditions. Synteny analysis and gene knockout revealed that two putative genes, hlyD-like tlr0903 (xcsB) and endoglucanase-like tlr1902 (xcsC), are linked to tll0007, although they are located apart from tll0007 in the T. vulcanus genome. Gene knockdown revealed that tlr1605 (tolC) was essential for the cellulose-mediated cell aggregation. Low temperature induced marked upregulation of tlr0903, and overexpression of both tlr0903 (but not tlr1902) and diguanylate cyclase resulted in the strong cell aggregation and cellulose accumulation under normal conditions. Based on these and phylogenetic analysis, we propose that the cyanobacterial extracellular cellulose production is due to a novel variant of the bacterial tripartite secretion system.

Tlr1612 is the major repressor of cell aggregation in the light-color-dependent c-di-GMP signaling network of Thermosynechococcus vulcanus

Cyclic diguanylate (c-di-GMP) is a bacterial second messenger involved in sessile/motile lifestyle transitions. We previously reported that c-di-GMP is a crucial inducer of cell aggregation of the cyanobacterium Thermosynechococcus vulcanus. The three cooperating cyanobacteriochrome photoreceptors (SesA/B/C) regulate cell aggregation in a light color-dependent manner by synthesizing/degrading c-di-GMP. Although a variety of c-di-GMP signaling proteins are encoded in cyanobacterial genomes, how c-di-GMP signaling networks are organized remains elusive. Here we experimentally demonstrate that the cellulose synthase Tll0007, which is essential for cell aggregation, binds c-di-GMP although the affinity is low (K_d = 63.9 ± 5.1 µM). We also show that SesA-the main trigger of cell aggregation-is subject to strict product feedback inhibition (IC50 = 1.07 ± 0.13 µM). These results suggest that SesA-produced c-di-GMP may not directly bind to Tll0007. We therefore systematically analyzed all 10 of the genes encoding proteins containing a c-di-GMP synthesis/degradation domain. We identified Tlr1612, harboring both domains, as the major repressor of cell aggregation under the repressing teal-green light irradiation. tlr1612 acts downstream of sesA and is not regulated transcriptionally by light color, suggesting that Tlr1612 may be involved in c-di-GMP amplification in the signaling cascade. Post-transcriptional control is likely crucial for the light-regulated c-di-GMP signaling.

Systematic Approaches to Efficiently Produce 2,3-Butanediol in a Marine Cyanobacterium

Cyanobacteria have attracted significant interest as a platform for renewable production of fuel and feedstock chemicals from abundant atmospheric carbon dioxide by way of photosynthesis. While great strides have been made in developing this technology in freshwater cyanobacteria, logistical issues remain in scale-up. Use of the cyanobacterium Synechococcus sp. PCC 7002 (7002) as a chemical production chassis could address a number of these issues given the higher tolerance to salt, light, and heat as well as the fast growth rate of 7002 in comparison to traditional model cyanobacteria such as Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803. However, despite growing interest, the development of genetic engineering tools for 7002 continues to lag behind those available for model cyanobacterial strains. In this work we demonstrate the systematic development of a 7002 production strain for the feedstock chemical 2,3-butanediol (23BD). We expand the range of tools available for use in 7002 by identifying and utilizing new integration sites for homologous recombination, demonstrating the inducibility of theophylline riboswitches, and screening a set of isopropyl β-d-1-thiogalactopyranoside (IPTG) inducible promoters. We then demonstrate improvements of 23BD production with the systematic screening of different conditions including: operon arrangement and copy number, light strength, inducer concentration, cell density at the time of induction, and nutrient concentration. Final production tests yielded titers of 1.6 g/L 23BD after 16 days at a rate of 100 mg/L/day. This work represents great strides in the development of 7002 as an industrially relevant production host.

Conjugates between photosystem I and a carbon nanotube for a photoresponse device

Photosystem I (PS I) is a large pigment-protein complex embedded in the thylakoid membranes that performs light-driven electron transfer across the thylakoid membrane. Carbon nanotubes exhibit excellent electrical conductivities and excellent strength and stiffness. In this study, we generated PSI-carbon nanotube conjugates dispersed in a solution aimed at application in artificial photosynthesis. PS I complexes in which a carbon nanotube binding peptide was introduced into the middle of the PsaE subunit were conjugated on a single-walled carbon nanotube, orienting the electron acceptor side to the nanotube. Spectral and photoluminescence analysis showed that the PS I is bound to a single-walled carbon nanotube, which was confirmed by transmission electron microscopy. Photocurrent observation proved that the photoexcited electron originated from PSI and transferred to the carbon nanotube with light irradiation, which also confirmed its orientated conjugation. The PS I-carbon nanotube conjugate will be a useful nano-optoelectronic device for the development of artificial systems.

Overcoming Intrinsic Restriction Enzyme Barriers Enhances Transformation Efficiency in Arthrospira platensis C1

The development of a reliable genetic transformation system for Arthrospira platensis has been a long-term goal, mainly for those trying either to improve its performance in large-scale cultivation systems or to enhance its value as food and feed additives. However, so far, most of the attempts to develop such a transformation system have had limited success. In this study, an efficient and stable transformation system for A. platensis C1 was successfully developed. Based on electroporation and transposon techniques, exogenous DNA could be transferred to and stably maintained in the A. platensis C1 genome. Most strains of Arthrospira possess strong restriction barriers, hampering the development of a gene transfer system for this group of cyanobacteria. By using a type I restriction inhibitor and liposomes to protect the DNA from nuclease digestion, the transformation efficiency was significantly improved. The transformants were able to grow on a selective medium for more than eight passages, and the transformed DNA could be detected from the stable transformants. We propose that the intrinsic endonuclease enzymes, particularly the type I restriction enzyme, in A. platensis C1 play an important role in the transformation efficiency of this industrial important cyanobacterium.

PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms

The identification of protein complexes is important for the understanding of protein structure and function and the regulation of cellular processes. We used blue-native PAGE and tandem mass spectrometry to identify protein complexes systematically, and built a web database, the protein co-migration database (PCoM-DB, http://pcomdb.lowtem.hokudai.ac.jp/proteins/top), to provide prediction tools for protein complexes. PCoM-DB provides migration profiles for any given protein of interest, and allows users to compare them with migration profiles of other proteins, showing the oligomeric states of proteins and thus identifying potential interaction partners. The initial version of PCoM-DB (launched in January 2013) included protein complex data for Synechocystis whole cells and Arabidopsis thaliana thylakoid membranes. Here we report PCoM-DB version 2.0, which includes new data sets and analytical tools. Additional data are included from whole cells of the pelagic marine picocyanobacterium Prochlorococcus marinus, the thermophilic cyanobacterium Thermosynechococcus elongatus, the unicellular green alga Chlamydomonas reinhardtii and the bryophyte Physcomitrella patens. The Arabidopsis protein data now include data for intact mitochondria, intact chloroplasts, chloroplast stroma and chloroplast envelopes. The new tools comprise a multiple-protein search form and a heat map viewer for protein migration profiles. Users can compare migration profiles of a protein of interest among different organelles or compare migration profiles among different proteins within the same sample. For Arabidopsis proteins, users can compare migration profiles of a protein of interest with putative homologous proteins from non-Arabidopsis organisms. The updated PCoM-DB will help researchers find novel protein complexes and estimate their evolutionary changes in the green lineage.

Sulfoquinovosyldiacylglycerol has an Essential Role in Thermosynechococcus elongatus BP-1 Under Phosphate-Deficient Conditions

Anionic lipids, sulfoquinovosyldiacylglycerol (SQDG) and phosphatidylglycerol (PG), are major classes of the thylakoid membrane lipids in cyanobacteria and plant chloroplasts. PG is essential for growth and photosynthesis of cyanobacteria, algae and plants, but the requirement for SQDG differs even among cyanobacterial species. Although SQDG and PG can compensate each other in part presumably to maintain proper balance of anionic charge in lipid bilayers, the functional relationship of these lipids is largely unknown. In this study, we inactivated the sqdB gene, encoding a UDP-sulfoquinovose synthase and involved in SQDG biosynthesis, in Thermosynechococcus elongatus BP-1. In wild-type cells, PG accounted for only approximately 3.5 mol% of total membrane lipids, but its content was substantially increased along with complete loss of SQDG in the sqdB mutant. Under phosphate (Pi)-sufficient conditions, the growth rate and PSII activity were slightly lower in sqdB than in wild-type cells. In addition, the formation of PSI trimers and PSII dimers and energy transfer in phycobilisomes were perturbed in the mutant. Under Pi-deficient conditions, the growth of sqdB cells was severely impaired, with a decrease in PSII activity. PG supplementation could partially rescue the defective growth and PSII activity of Pi-deficient sqdB cells but fully recovered the impaired growth of the pgsA mutant of T. elongatus, which is deficient in PG biosynthesis. These data suggest that SQDG has a specific role in the growth and photosynthesis of T. elongatus, which cannot be complemented by PG, particularly under Pi-deficient conditions.

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.

Modified molecular interactions of the pheophytin and plastoquinone electron acceptors in photosystem II of chlorophyll D-containing Acaryochloris marina as revealed by FTIR spectroscopy

Acaryochloris marina is a unique cyanobacterium that contains chlorophyll (Chl) d as a major pigment. Because Chl d has smaller excitation energy than Chl a used in ordinary photosynthetic organisms, the energetics of the photosystems of A. marina have been the subject of interest. It was previously shown that the redox potentials (E m's) of the redox-active pheophytin a (Pheo) and the primary plastoquinone electron acceptor (QA) in photosystem II (PSII) of A. marina are higher than those in Chl a-containing PSII, to compensate for the smaller excitation energy of Chl d (Allakhverdiev et al., Proc Natl Acad Sci USA 107: 3924-3929, 2010; ibid. 108: 8054-8058, 2011). To clarify the mechanisms of these E m increases, in this study, we have investigated the molecular interactions of Pheo and QA in PSII core complexes from A. marina using Fourier transform infrared (FTIR) spectroscopy. Light-induced FTIR difference spectra upon single reduction of Pheo and QA showed that spectral features in the regions of the keto and ester C=O stretches and the chlorin ring vibrations of Pheo and in the CO/CC stretching region of the Q A (-) semiquinone anion in A. marina are significantly different from those of the corresponding spectra in Chl a-containing cyanobacteria. These observations indicate that the molecular interactions, including the hydrogen bond interactions at the C=O groups, of these cofactors are modified in their binding sites of PSII proteins. From these results, along with the sequence information of the D1 and D2 proteins, it is suggested that A. marina tunes the E m's of Pheo and QA by altering nearby hydrogen bond networks to modify the structures of the binding pockets of these cofactors.

The 5 kDa protein NdhP is essential for stable NDH-1L assembly in Thermosynechococcus elongatus

The cyanobacterial NADPH:plastoquinone oxidoreductase complex (NDH-1), that is related to Complex I of eubacteria and mitochondria, plays a pivotal role in respiration as well as in cyclic electron transfer (CET) around PSI and is involved in a unique carbon concentration mechanism (CCM). Despite many achievements in the past, the complex protein composition and the specific function of many subunits of the different NDH-1 species remain elusive. We have recently discovered in a NDH-1 preparation from Thermosynechococcus elongatus two novel single transmembrane peptides (NdhP, NdhQ) with molecular weights below 5 kDa. Here we show that NdhP is a unique component of the ∼450 kDa NDH-1L complex, that is involved in respiration and CET at high CO₂ concentration, and not detectable in the NDH-1MS and NDH-1MS' complexes that play a role in carbon concentration. C-terminal fusion of NdhP with his-tagged superfolder GFP and the subsequent analysis of the purified complex by electron microscopy and single particle averaging revealed its localization in the NDH-1L specific distal unit of the NDH-1 complex, that is formed by the subunits NdhD1 and NdhF1. Moreover, NdhP is essential for NDH-1L formation, as this type of NDH-1 was not detectable in a ΔndhP::Km mutant.

Cyanobacteriochrome SesA is a diguanylate cyclase that induces cell aggregation in Thermosynechococcus

Cyanobacteria have unique photoreceptors, cyanobacteriochromes, that show diverse spectral properties to sense near-UV/visible lights. Certain cyanobacteriochromes have been shown to regulate cellular phototaxis or chromatic acclimation of photosynthetic pigments. Some cyanobacteriochromes have output domains involved in bacterial signaling using a second messenger cyclic dimeric GMP (c-di-GMP), but its role in cyanobacteria remains elusive. Here, we characterize the recombinant Tlr0924 from a thermophilic cyanobacterium Thermosynechococcus elongatus, which was expressed in a cyanobacterial system. The protein reversibly photoconverts between blue- and green-absorbing forms, which is consistent with the protein prepared from Escherichia coli, and has diguanylate cyclase activity, which is enhanced 38-fold by blue light compared with green light. Therefore, Tlr0924 is a blue light-activated diguanylate cyclase. The protein's relatively low affinity (10.5 mM) for Mg(2+), which is essential for diguanylate cyclase activity, suggests that Mg(2+) might also regulate c-di-GMP signaling. Finally, we show that blue light irradiation under low temperature is responsible for Thermosynechococcus vulcanus cell aggregation, which is abolished when tlr0924 is disrupted, suggesting that Tlr0924 mediates blue light-induced cell aggregation by producing c-di-GMP. Given our results, we propose the name "sesA (sessility-A)" for tlr0924. This is the first report for cyanobacteriochrome-dependent regulation of a sessile/planktonic lifestyle in cyanobacteria via c-di-GMP.

Crystal structure at 1.5Å resolution of the PsbV2 cytochrome from the cyanobacterium Thermosynechococcus elongatus

PsbV2 is a c-type cytochrome present in a very low abundance in the thermophilic cyanobacterium Thermosynechococcus elongatus. We purified this cytochrome and solved its crystal structure at a resolution of 1.5Å. The protein existed as a dimer in the crystal, and has an overall structure similar to other c-type cytochromes like Cytc6 and Cytc550, for example. However, the 5th and 6th heme iron axial ligands were found to be His51 and Cys101, respectively, in contrast to the more common bis-His or His/Met ligands found in most cytochromes. Although a few other c-type cytochromes were suggested to have this axial coordination, this is the first crystal structure reported for a c-type heme with this unusual His/Cys axial coordination. Previous spectroscopic characterizations of PsbV2 are discussed in relation to its structural properties.

Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement

BACKGROUND

Thermophilic microorganisms have special advantages for the conversion of plant biomass to fuels and chemicals. Members of the genus Caldicellulosiruptor are the most thermophilic cellulolytic bacteria known. They have the ability to grow on a variety of non-pretreated biomass substrates at or near ~80°C and hold promise for converting biomass to bioproducts in a single step. As for all such relatively uncharacterized organisms with desirable traits, the ability to genetically manipulate them is a prerequisite for making them useful. Metabolic engineering of pathways for product synthesis is relatively simple compared to engineering the ability to utilize non-pretreated biomass.

RESULTS

Here we report the construction of a deletion of cbeI (Cbes2438), which encodes a restriction endonuclease that is as a major barrier to DNA transformation of C. bescii. This is the first example of a targeted chromosomal deletion generated by homologous recombination in this genus and the resulting mutant, JWCB018 (ΔpyrFA ΔcbeI), is readily transformed by DNA isolated from E. coli without in vitro methylation. PCR amplification and sequencing suggested that this deletion left the adjacent methyltransferase (Cbes2437) intact. This was confirmed by the fact that DNA isolated from JWCB018 was protected from digestion by CbeI and HaeIII. Plasmid DNA isolated from C. hydrothermalis transformants were readily transformed into C. bescii. Digestion analysis of chromosomal DNA isolated from seven Caldicellulosiruptor species by using nine different restriction endonucleases was also performed to identify the functional restriction-modification activities in this genus.

CONCLUSION

Deletion of the cbeI gene removes a substantial barrier to routine DNA transformation and chromosomal modification of C. bescii. This will facilitate the functional analyses of genes as well as metabolic engineering for the production of biofuels and bioproducts from biomass. An analysis of restriction-modification activities in members of this genus suggests a way forward to eliminating restriction as a barrier to DNA transformation and efficient genetic manipulation of this important group of hyperthermophiles.

Bioengineering of carbon fixation, biofuels, and biochemicals in cyanobacteria and plants

Development of sustainable energy is a pivotal step towards solutions for today's global challenges, including mitigating the progression of climate change and reducing dependence on fossil fuels. Biofuels derived from agricultural crops have already been commercialized. However the impacts on environmental sustainability and food supply have raised ethical questions about the current practices. Cyanobacteria have attracted interest as an alternative means for sustainable energy productions. Being aquatic photoautotrophs they can be cultivated in non-arable lands and do not compete for land for food production. Their rich genetic resources offer means to engineer metabolic pathways for synthesis of valuable bio-based products. Currently the major obstacle in industrial-scale exploitation of cyanobacteria as the economically sustainable production hosts is low yields. Much effort has been made to improve the carbon fixation and manipulating the carbon allocation in cyanobacteria and their evolutionary photosynthetic relatives, algae and plants. This review aims at providing an overview of the recent progress in the bioengineering of carbon fixation and allocation in cyanobacteria; wherever relevant, the progress made in plants and algae is also discussed as an inspiration for future application in cyanobacteria.

Deletion of psbJ leads to accumulation of Psb27-Psb28 photosystem II complexes in Thermosynechococcus elongatus

The life cycle of Photosystem II (PSII) is embedded in a network of proteins that guides the complex through biogenesis, damage and repair. Some of these proteins, such as Psb27 and Psb28, are involved in cofactor assembly for which they are only transiently bound to the preassembled complex. In this work we isolated and analyzed PSII from a ΔpsbJ mutant of the thermophilic cyanobacterium Thermosynechococcus elongatus. From the four different PSII complexes that could be separated the most prominent one revealed a monomeric Psb27-Psb28 PSII complex with greatly diminished oxygen-evolving activity. The MALDI-ToF mass spectrometry analysis of intact low molecular weight subunits (<10kDa) depicted wild type PSII with the absence of PsbJ. Relative quantification of the PsbA1/PsbA3 ratio by LC-ESI mass spectrometry using (15)N labeled PsbA3-specific peptides indicated the complete replacement of PsbA1 by the stress copy PsbA3 in the mutant, even under standard growth conditions (50μmol photons m(-2) s(-1)). This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.

Role of novel dimeric Photosystem II (PSII)-Psb27 protein complex in PSII repair

The multisubunit membrane protein complex Photosystem II (PSII) catalyzes one of the key reactions in photosynthesis: the light-driven oxidation of water. Here, we focus on the role of the Psb27 assembly factor, which is involved in biogenesis and repair after light-induced damage of the complex. We show that Psb27 is essential for the survival of cyanobacterial cells grown under stress conditions. The combination of cold stress (30 °C) and high light stress (1000 μmol of photons × m(-2) × s(-1)) led to complete inhibition of growth in a Δpsb27 mutant strain of the thermophilic cyanobacterium Thermosynechococcus elongatus, whereas wild-type cells continued to grow. Moreover, Psb27-containing PSII complexes became the predominant PSII species in preparations from wild-type cells grown under cold stress. Two different PSII-Psb27 complexes were isolated and characterized in this study. The first complex represents the known monomeric PSII-Psb27 species, which is involved in the assembly of PSII. Additionally, a novel dimeric PSII-Psb27 complex could be allocated in the repair cycle, i.e. in processes after inactivation of PSII, by (15)N pulse-label experiments followed by mass spectrometry analysis. Comparison with the corresponding PSII species from Δpsb27 mutant cells showed that Psb27 prevented the release of manganese from the previously inactivated complex. These results indicate a more complex role of the Psb27 protein within the life cycle of PSII, especially under stress conditions.

Cellulose accumulation and a cellulose synthase gene are responsible for cell aggregation in the cyanobacterium Thermosynechococcus vulcanus RKN

A thermophilic cyanobacterium, Thermosynechococcus vulcanus RKN, exhibits cell aggregation under low temperature illuminated conditions as a means of physiological acclimation to avoid excess light stress. The cell aggregation was dispersed with cellulase treatment. We developed a method to quantify small amounts of cellulose by partial cellulose purification followed by quantitation of liberated glucose by cellulase. Under low temperature illuminated light conditions, cellulose accumulation was induced approximately 2-fold, to 10 μg (4 × 10(9) cells)(-1), and slightly preceded aggregation. Based on sequence similarity, three candidate genes for cellulose synthase (Tvtll0007, Tvtlr1795 and Tvtlr1930-33) were cloned from T. vulcanus. Gene disruption analysis showed that only Tvtll0007 was responsible for both the light- and low temperature-induced cell aggregation and the induction of cellulose accumulation. Gene expression analysis suggested that the low temperature illuminated conditions quickly induced expression of Tvtlr1795 and Tvtlr1930-33, while the induction of Tvtll0007 was slow. These results suggest that Tvtll0007 encodes a functional cellulose synthase whose activity may not be regulated at the transcriptional level.

Genetic tool development underpins recent advances in thermophilic whole-cell biocatalysts

The environmental value of sustainably producing bioproducts from biomass is now widely appreciated, with a primary target being the economic production of fuels such as bioethanol from lignocellulose. The application of thermophilic prokaryotes is a rapidly developing niche in this field, driven by their known catabolic versatility with lignocellulose-derived carbohydrates. Fundamental to the success of this work has been the development of reliable genetic and molecular systems. These technical tools are now available to assist in the development of other (hyper)thermophilic strains with diverse phenotypes such as hemicellulolytic and cellulolytic properties, branched chain alcohol production and other 'valuable bioproduct' synthetic capabilities. Here we present an insight into the historical limitations, recent developments and current status of a number of genetic systems for thermophiles. We also highlight the value of reliable genetic methods for increasing our knowledge of thermophile physiology. We argue that the development of robust genetic systems is paramount in the evolution of future thermophilic based bioprocesses and make suggestions for future approaches and genetic targets that will facilitate this process.

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.

The PsbK subunit is required for the stable assembly and stability of other small subunits in the PSII complex in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1

PsbK is a small membrane protein of the PSII core complex and is highly conserved from cyanobacteria to plants. Here, we studied its role in the thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1, by focusing on a psbK disruptant with hexahistidine-tagged CP47. The psbK disruptant showed photoautotrophic growth comparable with that of the wild type under a wide range of light conditions. The mutant PSII complex retained the oxygen-evolving activity with a unique modification of the acceptor Q(B) site. N-terminal sequencing revealed that Ycf12 and PsbZ proteins were lost in the PSII complex prepared from the mutant. Immunoblotting detected reduced accumulation of PsbZ in the mutant thylakoid. These results suggest that PsbK is required not only for association of PsbZ and Ycf12 with the isolated PSII complex but also for the stabilization of PsbZ in the thylakoid membrane.

Engineering clostridium strain to accept unmethylated DNA

It is difficult to genetically manipulate the medically and biotechnologically important genus Clostridium due to the existence of the restriction and modification (RM) systems. We identified and engineered the RM system of a model clostridial species, C. acetobutylicum, with the aim to allow the host to accept the unmethylated DNA efficiently. A gene CAC1502 putatively encoding the type II restriction endonuclease Cac824I was identified from the genome of C. acetobutylicum DSM1731, and disrupted using the ClosTron system based on group II intron insertion. The resulting strain SMB009 lost the type II restriction endonuclease activity, and can be transformed with unmethylated DNA as efficiently as with methylated DNA. The strategy reported here makes it easy to genetically modify the clostridial species using unmethylated DNA, which will help to advance the understanding of the clostridial physiology from the molecular level.

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.

Absence of the PsbZ subunit prevents association of PsbK and Ycf12 with the PSII complex in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1

PsbZ (Ycf9) is a membrane protein of PSII complexes and is highly conserved from cyanobacteria to plants. We deleted the psbZ gene in the thermophilic cyanobacterium, Thermosynechococcus elongatus. The mutant cells showed photoautotrophic growth indistinguishable from that of the wild type under low and standard light conditions, while they showed even better growth than the wild type under high light. The mutant accumulated less carotenoids and more phycobiliproteins than the wild type under high light, suggestive of tolerance to photoinhibition. The mutant cells evolved oxygen at a rate comparable with the wild type, while the PSII complex isolated from the mutant retained much lower activity than the wild type. N-terminal sequencing revealed that Ycf12 and PsbK proteins were almost lost in the PSII complex. These results indicate that PsbZ is involved in functional integrity of the PSII complex by stabilizing PsbK and Ycf12. We suggest that Ycf12 is an unidentified membrane-spanning polypeptide that is placed near PsbZ and PsbK in the crystal structure of PSII.

Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events

Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between cyanobacteria and other phyla. A novel method of detecting and enumerating potential horizontal gene transfer events within a group of organisms based on analyses of "embedded quartets" allows us to identify phylogenetic signal consistent with a plurality of gene families, as well as to delineate cases of conflict to the plurality signal, which include horizontally transferred genes. To infer horizontal gene transfer events between cyanobacteria and other phyla, we added homologs from 168 available genomes. We screened phylogenetic trees reconstructed for each of these extended gene families for highly supported monophyly of cyanobacteria (or lack of it). Cyanobacterial genomes reveal a complex evolutionary history, which cannot be represented by a single strictly bifurcating tree for all genes or even most genes, although a single completely resolved phylogeny was recovered from the quartets' plurality signals. We find more conflicts within cyanobacteria than between cyanobacteria and other phyla. We also find that genes from all functional categories are subject to transfer. However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases.

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.