The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803.

Cyanobacteria exhibit a great capacity to adapt to different environmental conditions through changes in gene expression. Although this plasticity has been extensively studied in the model cyanobacterium Synechocystis sp. PCC 6803, a detailed analysis of the coordinated transcriptional adaption across varying conditions is lacking. Here, we report a meta-analysis of 756 individual microarray measurements conducted in 37 independent studies-the most comprehensive study of the Synechocystis transcriptome to date. Using stringent statistical evaluation, we characterized the coordinated adaptation of Synechocystis' gene expression on systems level. Evaluation of the data revealed that the photosynthetic apparatus is subjected to greater changes in expression than other cellular components. Nevertheless, network analyses indicated a significant degree of transcriptional coordination of photosynthesis and various metabolic processes, and revealed the tight co-regulation of components of photosystems I, II and phycobilisomes. Detailed inspection of the integrated data led to the discovery a variety of regulatory patterns and novel putative photosynthetic genes. Intriguingly, global clustering analyses suggested contrasting transcriptional response of metabolic and regulatory genes stress to conditions. The integrated Synechocystis transcriptome can be accessed and interactively analyzed via the CyanoEXpress website (http://cyanoexpress.sysbiolab.eu)

Fluorescence as a tool to understand changes in photosynthetic electron flow regulation

International audienceThe physiological state of a chloroplast is stronglyinfluenced by both biotic and abiotic conditions.Unfavourable growth conditions lead to photosyntheticstress. Chlorophyll a fluorescence is a widelyused probe of photosynthetic activity (specificallyPSII), and therefore stress which specifically targetsthe electron transport pathway and associated alternativeelectron cycling pathways. By manipulating theprocesses that control photosynthesis, affecting thechlorophyll a fluorescence, yields detailed insight intothe biochemicalpathways. Light that is captured by achlorophyll molecule can be utilised in three competingprocesses; electron transport, energy dissipation(via heat) and chlorophyll a fluorescence emission.Electrons produced by water-splitting are not alwaysused in carbon fixation; if the incident irradiancegeneratesmore electrons than the dark reactionscan use in carbon fixation, damage will occur to the photosynthetic apparatus. If carbon fixation is inhibitedby temperature or reduced inorganic carbon (Ci), ATPor NADPH availability, then the photosystem dynamicallyadjusts and uses alternate sinks for electrons, suchas molecular oxygen (water-water cycle or Mehler ascorbateperoxidase reaction). The process of stress acclimationleads to a number of photoprotective pathwaysand we describe how inhibitors can be used to identifythese particular processes. In this chapter, we describethe processes controlling electron transport as influencedby light-induced stress

Detection of the enzymatically-active polyhydroxyalkanoate synthase subunit gene, phaC, in cyanobacteria via colony PCR

A colony PCR-based assay was developed to rapidly determine if a cyanobacterium of interest contains the requisite genetic material, the PHA synthase PhaC subunit, to produce polyhydroxyalkanoates (PHAs). The test is both high throughput and robust, owing to an extensive sequence analysis of cyanobacteria PHA synthases. The assay uses a single detection primer set and a single reaction condition across multiple cyanobacteria strains to produce an easily detectable positive result - amplification via PCR as evidenced by a band in electrophoresis. In order to demonstrate the potential of the presence of phaC as an indicator of a cyanobacteria\u27s PHA accumulation capabilities, the ability to produce PHA was assessed for five cyanobacteria with a traditional in vivo PHA granule staining using an oxazine dye. The confirmed in vivo staining results were then compared to the PCR-based assay results and found to be in agreement. The colony PCR assay was capable of successfully detecting the phaC gene in all six of the diverse cyanobacteria tested which possessed the gene, while exhibiting no undesired product formation across the nine total cyanobacteria strains tested. The colony PCR quick prep provides sufficient usable DNA template such that this assay could be readily expanded to assess multiple genes of interest simultaneously

Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis

The relationship between tunicates and the uncultivated cyanobacterium Prochloron didemni has long provided a model symbiosis. P. didemni is required for survival of animals such as Lissoclinum patella and also makes secondary metabolites of pharmaceutical interest. Here, we present the metagenomes, chemistry, and microbiomes of four related L. patella tunicate samples from a wide geographical range of the tropical Pacific. The remarkably similar P. didemni genomes are the most complex so far assembled from uncultivated organisms. Although P. didemni has not been stably cultivated and comprises a single strain in each sample, a complete set of metabolic genes indicates that the bacteria are likely capable of reproducing outside the host. The sequences reveal notable peculiarities of the photosynthetic apparatus and explain the basis of nutrient exchange underlying the symbiosis. P. didemni likely profoundly influences the lipid composition of the animals by synthesizing sterols and an unusual lipid with biofuel potential. In addition, L. patella also harbors a great variety of other bacterial groups that contribute nutritional and secondary metabolic products to the symbiosis. These bacteria possess an enormous genetic potential to synthesize new secondary metabolites. For example, an antitumor candidate molecule, patellazole, is not encoded in the genome of Prochloron and was linked to other bacteria from the microbiome. This study unveils the complex L. patella microbiome and its impact on primary and secondary metabolism, revealing a remarkable versatility in creating and exchanging small molecules

Comparative analysis of thylakoid protein complexes in the mesophyll and bundle sheath cells from C 3

To better understand the coordination between dark and light reactions during the transition from C3 to C4 photosynthesis, we optimized a method for separating thylakoids from mesophyll (MC) and bundle sheath cells (BSC) across different plant species. We grew six Paniceae grasses including representatives from the C3, C3‐C4 and C4photosynthetic types and all three C4 biochemical subtypes (NADP‐ME, NAD‐ME and PEPCK) in addition to Zea mays under control conditions (1000 μmol quanta m‐2 s‐1 and 400 ppm of CO2). Proteomics analysis of thylakoids under native conditions, using BN‐PAGE followed by LC/MS, demonstrated the presence of subunits of all light‐reaction related complexes in all species and cell types. C4 NADP‐ME species showed a higher PSI/PSII ratio and a clear accumulation of NDH complexes in BSCs, while Cytb6f was more abundant in BSCs of C4 NAD‐ME species. The C4 PEPCK species showed no clear differences between cell types. Our study presents, for the first time, a good separation between BSC and MC for a C3‐C4 intermediate grass which did not show noticeable differences in the distribution of the thylakoid complexes. For the NADP‐ME species P. antidotale, growth at glacial CO2 (180 ppm of CO2) had no effect on the distribution of the light‐reaction complexes, while growth at low light (200 μmol quanta m‐2 s‐1) promoted the accumulation of light‐harvesting proteins in both cell types. These results add to our understanding of thylakoid distribution across photosynthetic types and subtypes, and introduce thylakoid distribution between the MC and BSC of a C3‐C4 intermediate species