SciCombinator

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Concept: Synechocystis

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Bacterial phototaxis was first recognized over a century ago, but the method by which such small cells can sense the direction of illumination has remained puzzling. The unicellular cyanobacterium Synechocystis sp. PCC 6803 moves with Type IV pili and measures light intensity and color with a range of photoreceptors. Here, we show that individual Synechocystis cells do not respond to a spatiotemporal gradient in light intensity, but rather they directly and accurately sense the position of a light source. We show that directional light sensing is possible because Synechocystis cells act as spherical microlenses, allowing the cell to see a light source and move towards it. A high-resolution image of the light source is focused on the edge of the cell opposite to the source, triggering movement away from the focused spot. Spherical cyanobacteria are probably the world’s smallest and oldest example of a camera eye.

Concepts: DNA, Cyanobacteria, Archaea, Bacteria, Organism, Light, Synechocystis, Pilus

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Abstract In the present economy, difficulties to access energy sources are real drawbacks to maintain our current lifestyle. In fact, increasing interests have been gathered around efficient strategies to use energy sources that do not generate high CO2 titers. Thus, science-funding agencies have invested more resources into research on hydrogen among other biofuels as interesting energy vectors. This article reviews present energy challenges and frames it into the present fuel usage landscape. Different strategies for hydrogen production are explained and evaluated. Focus is on biological hydrogen production; fermentation and photon-fuelled hydrogen production are compared. Mathematical models in biology can be used to assess, explore and design production strategies for industrially relevant metabolites, such as biofuels. We assess the diverse construction and uses of genome-scale metabolic models of cyanobacterium Synechocystis sp. PCC6803 to efficiently obtain biofuels. This organism has been studied as a potential photon-fuelled production platform for its ability to grow from carbon dioxide, water and photons, on simple culture media. Finally, we review studies that propose production strategies to weigh this organism’s viability as a biofuel production platform. Overall, the work presented in this review unveils the industrial capabilities of cyanobacterium Synechocystis sp. PCC6803 to evolve interesting metabolites as a clean biofuel production platform.

Concepts: Oxygen, Carbon dioxide, Metabolism, Hydrogen, Yeast, Synechocystis, Hydrogen production, Biological hydrogen production

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BACKGROUND: The transcriptomes of several cyanobacterial strains have been shown to exhibit diurnal oscillation patterns, reflecting the diurnal phototrophic lifestyle of the organisms.The analysis of such genome-wide transcriptional oscillations is often facilitated by the use of clustering algorithms in conjunction with a number of pre-processing steps. Biological interpretation is usually focussed on the time and phase of expression of the resulting groups of genes.However, the use of microarray technology in such studies requires the normalization of pre-processing data, with unclear impact on the qualitative and quantitative features of the derived information on the number of oscillating transcripts and their respective phases. RESULTS: A microarray based evaluation of diurnal expression in the cyanobacterium Synechocystis sp. PCC 6803 is presented. As expected, the temporal expression patterns reveal strong oscillations in transcript abundance.We compare the Fourier transformation-based expression phase before and after the application of quantile normalization, median polishing, cyclical LOESS, and least oscillating set (LOS) normalization.Whereas LOS normalization mostly preserves the phases of the raw data, the remaining methods introduce systematic biases. In particular, quantile-normalization is found to introduce a phase-shift of 180°, effectively changing night-expressed genes into day-expressed ones. Comparison of a large number of clustering results of differently normalized data shows that the normalization method determines the result. Subsequent steps, such as the choice of data transformation, similarity measure, and clustering algorithm, only play minor roles.We find that the standardization and the DTF transformation are favorable for the clustering of time series in contrast to the 12m transformation. We use the cluster-wise functional enrichment of a clustering derived by LOS normalization, clustering using flowClust, and DFT transformation to derive the diurnal biological program of Synechocystis sp.. CONCLUSION: Application of quantile normalization, median polishing, and also cyclic LOESS normalization of the presented cyanobacterial dataset lead to increased numbers of oscillating genes and the systematic shift of the expression phase. The LOS normalization minimizes the observed detrimental effects. As previous analyses employed a variety of different normalization methods, a direct comparison of results must be treated with caution.

Concepts: Cyanobacteria, Gene, Gene expression, Transcription, Molecular biology, Oscillation, Synechocystis, Seasonality

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Environmental cues can stimulate a variety of single-cell responses, as well as collective behaviors that emerge within a bacterial community. These responses require signal integration and transduction, which can occur on a variety of time scales and often involve feedback between processes, for example, between growth and motility. Here, we investigate the dynamics of responses of the phototactic, unicellular cyanobacterium Synechocystis sp. PCC6803 to complex light inputs that simulate the natural environments that cells typically encounter. We quantified single-cell motility characteristics in response to light of different wavelengths and intensities. We found that red and green light primarily affected motility bias rather than speed, while blue light inhibited motility altogether. When light signals were simultaneously presented from different directions, cells exhibited phototaxis along the vector sum of the light directions, indicating that cells can sense and combine multiple signals into an integrated motility response. Under a combination of antagonistic light signal regimes (phototaxis-promoting green light and phototaxis-inhibiting blue light), the ensuing bias was continuously tuned by competition between the wavelengths, and the community response was dependent on both bias and cell growth. The phototactic dynamics upon a rapid light shift revealed a wavelength dependence on the time scales of photoreceptor activation/deactivation. Thus, Synechocystis cells achieve exquisite integration of light inputs at the cellular scale through continuous tuning of motility, and the pattern of collective behavior depends on single-cell motility and population growth.IMPORTANCE The photosynthetic cyanobacterium Synechocystis sp. exhibits phototaxis that is dependent on the incident light wavelength through the action of various photoreceptors. In natural environments, cells experience a set of highly dynamic and complex light inputs, yet how cells transduce multiple or dynamic inputs into motion is unknown. In this study, we measured the phototactic behaviors of single cells and communities as a function of light intensity or when illuminated by combinations of lights of different wavelengths or incidence directions. Responses to a spectrum of light regimes revealed that Synechocystis sp. integrates information about the light environment to tune its phototactic response, which is likely generated by competition among photoreceptors and the degree of wavelength-regulated growth to sensitively control the direction and degree of movement.

Concepts: Cyanobacteria, Photosynthesis, Bacteria, Light, Electromagnetic radiation, Wavelength, Synechocystis, Visible spectrum

1

Bacterial toxin-antitoxin (TA) systems are genetic elements, which are encoded by plasmid as well as chromosomal loci and mediate plasmid and genomic island maintenance through post-segregational killing mechanisms. TA systems exist in surprisingly high numbers in all prokaryotes, but cyanobacterial TA systems have been only very poorly experimentally characterized so far. Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. As such, cyanobacteria are of high ecological importance and are considered promising for the production of biofuels. Here, we present the molecular characterization of the sll7003/ssl7004 TA system encoded on plasmid pSYSA of the model cyanobacterium Synechocystis sp. PCC 6803 as involving a Mg2+-dependent RNA endonuclease activity targeting single-stranded RNA regions and demonstrate the functionality of four more TA systems encoded on this 100,749 bp plasmid. Furthermore, one additional type I, one additional type II and three free-standing TA system components are predicted on pSYSA, all of which appear active judged by their expression. By harboring at least seven simultaneously active TA systems, pSYSA appears as the plasmid most strongly selected for among all plasmids studied in this respect thus far. These results point to a high biological relevance of pSYSA, whose coding capacity is to 75% devoted to three distinct CRISPR systems mediating antiviral defense.

Concepts: DNA, Cyanobacteria, Gene, Genetics, Bacteria, Molecular biology, Genome, Synechocystis

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Small CAB-like proteins (SCPs) are single-helix light-harvesting-like proteins found in all organisms performing oxygenic photosynthesis. We investigated the effect of growth in moderate salt stress on these stress-induced proteins in the cyanobacterium Synechocystis sp. PCC 6803 depleted of Photosystem I (PSI), which expresses SCPs constitutively, and compared these cells with a PSI-less/ScpABCDE(-) mutant. SCPs, by stabilizing chlorophyll-binding proteins and Photosystem II (PSII) assembly, protect PSII from photoinhibitory damages, and in their absence electrons accumulate and will lead to ROS formation. The presence of 0.2 M NaCl in the growth medium increased the respiratory activity and other PSII electron sinks in the PSI-less/ScpABCDE(-) strain. We postulate that this salt-induced effect consumes the excess of PSII-generated electrons, reduces the pressure of the electron transport chain, and thereby prevents (1)O2 production.

Concepts: Cyanobacteria, Photosynthesis, Bacteria, Metabolism, Cellular respiration, Photosystem, Synechocystis, Oxygen evolution

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Cyanobacteria perform photosynthesis with the use of large light-harvesting antennae called phycobilisomes (PBSs). These hemispherical PBSs contain hundreds of open-chain tetrapyrrole chromophores bound to different peptides, providing an arrangement in which excitation energy is funnelled towards the PBS core from where it can be transferred to photosystem I and/or photosystem II. In the PBS core, many allophycocyanin (APC) trimers are present, red-light-absorbing phycobiliproteins that covalently bind phycocyanobilin (PCB) chromophores. APC trimers were amongst the first light-harvesting complexes to be crystallized. APC trimers have two spectrally different PCBs per monomer, a high- and a low-energy pigment. The crystal structure of the APC trimer reveals the close distance (~21 Å) between those two chromophores (the distance within one monomer is ~51 Å) and this explains the ultrafast (~1 ps) excitation energy transfer (EET) between them. Both chromophores adopt a somewhat different structure, which is held responsible for their spectral difference. Here we used spectrally resolved picosecond fluorescence to study EET in these APC trimers both in crystallized and in solubilized form. We found that not all closely spaced pigment couples consist of a low- and a high-energy pigment. In ~10% of the cases, a couple consists of two high-energy pigments. EET to a low-energy pigment, which can spectrally be resolved, occurs on a time scale of tens of picoseconds. This transfer turns out to be three times faster in the crystal than in the solution. The spectral characteristics and the time scale of this transfer component are similar to what have been observed in the whole cells of Synechocystis sp. PCC 6803, for which it was ascribed to EET from C-phycocyanin to APC. The present results thus demonstrate that part of this transfer should probably also be ascribed to EET within APC trimers.

Concepts: Cyanobacteria, Time, Photosynthesis, Crystal, Photosystem, Photosystem I, Synechocystis, Phycobilin

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The sll1981 protein from cyanobacterium Synechocystis sp. PCC6803 had been reported to exhibit acetolactate synthase (ALS) and L-myo-inositol-1-phosphate synthase (MIPS) activities previously. Based on amino acids sequences alignment, sll1981 protein was postulated to function as α-ketoglutarate decarboxylase (α-KGD), which played important role in completing cyanobacterial tricarboxylic acid (TCA) cycle. However the detailed enzymatic kinetics of sll1981 as ALS, MIPS and α-KGD were not determined yet. In this study, the recombinant sll1981 protein was purified from supernatant of E. coli cell and the substrate specificity of sll1981 towards pyruvate, D-glucose-6-phosphate and α-ketoglutarate was examined using homogenous recombinant sll1981. Steady-state kinetics results showed that sll1981 was a dual functional enzyme, which displayed much higher activity as α-KGD than as ALS. At the same time the MIPS activity of sll1981 was not detectable, although it was reported to be as MIPS previously. These findings not only confirmed the previous statement of the function of sll1981 as ALS and disputed the claimed function of sll1981 as MIPS, but also affirmed the new function of sll1981 as α-KGD. Therefore sll1981 was probably a key enzyme in completing the TCA cycle of Synechocystis sp. PCC6803.

Concepts: Enzyme kinetics, Protein, Cell, Amino acid, Acid, Enzyme, Escherichia coli, Synechocystis

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Cyanobacterial phycobilisome (PBS) pigment-protein complexes harvest light and transfer the energy to reaction centers. Previous ensemble studies have shown that cyanobacteria respond to changes in nutrient availability by modifying the structure of PBS complexes, but this process has not been visualized for individual pigments at the single-cell level due to spectral overlap. We characterized the response of four key photosynthetic pigments to nitrogen depletion and repletion at the subcellular level in individual, live Synechocystis sp. PCC 6803 cells using hyperspectral confocal fluorescence microscopy and multivariate image analysis. Our results revealed that PBS degradation and re-synthesis comprise a rapid response to nitrogen fluctuations, with coordinated populations of cells undergoing pigment modifications. Chlorophyll fluorescence originating from photosystem I and II decreased during nitrogen starvation, but no alteration in subcellular chlorophyll localization was found. We observed differential rod and core pigment responses to nitrogen deprivation, suggesting that PBS complexes undergo a stepwise degradation process.

Concepts: Cyanobacteria, Photosynthesis, Bacteria, Plant, Nitrogen fixation, Photosystem, Chlorophyll, Synechocystis

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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.

Concepts: DNA, Cyanobacteria, Photosynthesis, Oxygen, Carbon dioxide, Genetics, Chemistry, Synechocystis