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).

• Publication year

  2016

• Venue

  Scientific Reports

• Publication date

  2016-02-29

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/srep22168PMID 26923200PMCID 4770689
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Attachment of phycobilisomes in an antenna–photosystem I supercomplex of cyanobacteria

  2014cited by this paper
• Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

  2014cited by this paper
• Removal of both Ycf48 and Psb27 in Synechocystis sp. PCC 6803 disrupts Photosystem II assembly and alters QA − oxidation in the mature complex

  2014cited by this paper
• Discovery of a Chlorophyll Binding Protein Complex Involved in the Early Steps of Photosystem II Assembly in Synechocystis[W]

  2014cited by this paper
• Two essential FtsH proteases control the level of the Fur repressor during iron deficiency in the cyanobacterium Synechocystis sp. PCC 6803

  2014cited by this paper
• Reverse genetics in complex multigene operons by co-transformation of the plastid genome and its application to the open reading frame previously designated psbN.

  2013cited by this paper
• Phycobilisomes Supply Excitations to Both Photosystems in a Megacomplex in Cyanobacteria

  2013influential reference
• Thylakoid Terminal Oxidases Are Essential for the Cyanobacterium Synechocystis sp. PCC 6803 to Survive Rapidly Changing Light Intensities1[C][W][OA]

  2013cited by this paper
• CyanoEXpress: A web database for exploration and visualisation of the integrated transcriptome of cyanobacterium Synechocystis sp. PCC6803

  2012cited by this paper
• Identical Hik-Rre systems are involved in perception and transduction of salt signals and hyperosmotic signals but regulate the expression of individual genes to different extents in Synechocystis.

  2012cited by this paper
• Iron Deprivation in Synechocystis: Inference of Pathways, Non-coding RNAs, and Regulatory Elements from Comprehensive Expression Profiling

  2012cited by this paper
• Positive Regulation of psbA Gene Expression by cis-Encoded Antisense RNAs in Synechocystis sp. PCC 68031[OA]

  2012cited by this paper
• Transcriptomic responses of Synechocystis sp. PCC 6803 encapsulated in silica gel

  2012cited by this paper
• shRNAPred (version 1.0): An open source and standalone software for short hairpin RNA (shRNA) prediction

  2012cited by this paper
• The Psb27 Assembly Factor Binds to the CP43 Complex of Photosystem II in the Cyanobacterium Synechocystis sp. PCC 68031[C][W][OA]

  2011cited by this paper
• Cyanobacterial NDH-1 complexes: novel insights and remaining puzzles.

  2011cited by this paper
• Synthetic biology in cyanobacteria engineering and analyzing novel functions.

  2011cited by this paper
• Concerted Changes in Gene Expression and Cell Physiology of the Cyanobacterium Synechocystis sp. Strain PCC 6803 during Transitions between Nitrogen and Light-Limited Growth1[W][OA]

  2011cited by this paper
• The small CAB-like proteins of the cyanobacterium Synechocystis sp. PCC 6803: their involvement in chlorophyll biogenesis for Photosystem II.

  2011cited by this paper
• Methods for part/device characterization and chassis engineering

  2011cited by this paper
• Serine/Threonine Protein Kinase SpkG Is a Candidate for High Salt Resistance in the Unicellular Cyanobacterium Synechocystis sp. PCC 6803

  2011cited by this paper
• Photosystem II Component Lifetimes in the Cyanobacterium Synechocystis sp. Strain PCC 6803

  2011cited by this paper
• Comparison and consolidation of microarray data sets of human tissue expression

  2010cited by this paper
• Identification of Components Associated with Thermal Acclimation of Photosystem II in Synechocystis sp. PCC6803

  2010cited by this paper
• Recent advances in understanding the assembly and repair of photosystem II.

  2010cited by this paper
• Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium

  2010cited by this paper
• Purification and characterization of photosystem I complex from Synechocystis sp. PCC 6803 by expressing histidine-tagged subunits.

  2010cited by this paper
• Simultaneous Inactivation of Sigma Factors B and D Interferes with Light Acclimation of the Cyanobacterium Synechocystis sp. Strain PCC 6803

  2009cited by this paper
• Evidence for a major role of antisense RNAs in cyanobacterial gene regulation

  2009cited by this paper
• DNA supercoiling regulates the stress-inducible expression of genes in the cyanobacterium Synechocystis.

  2009cited by this paper
• Integration of Carbon and Nitrogen Metabolism with Energy Production Is Crucial to Light Acclimation in the Cyanobacterium Synechocystis1[W][OA]

  2008cited by this paper
• Reassessing the first appearance of eukaryotes and cyanobacteria

  2008cited by this paper
• Consensus and Meta-analysis regulatory networks for combining multiple microarray gene expression datasets

  2008cited by this paper
• Low-oxygen induction of normally cryptic psbA genes in cyanobacteria.

  2008cited by this paper
• The cyanobacterial homologue of the RNA chaperone Hfq is essential for motility of Synechocystis sp. PCC 6803.

  2008cited by this paper
• Association of small CAB-like proteins (SCPs) of Synechocystis sp. PCC 6803 with Photosystem II

  2008cited by this paper
• Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803

  2008cited by this paper
• High Sensitivity Proteomics Assisted Discovery of a Novel Operon Involved in the Assembly of Photosystem II, a Membrane Protein Complex*

  2008cited by this paper
• PetG and PetN, but not PetL, are essential subunits of the cytochrome b6f complex from Synechocystis PCC 6803.

  2007cited by this paper
• Cadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator

  2007cited by this paper
• Localization of the Small CAB-like Proteins in Photosystem II*

  2007cited by this paper
• Late Assembly Steps and Dynamics of the Cyanobacterial Photosystem I*

  2007cited by this paper
• Structure and function of RbcX, an assembly chaperone for hexadecameric Rubisco.

  2007cited by this paper
• The role of the FtsH and Deg proteases in the repair of UV-B radiation-damaged Photosystem II in the cyanobacterium Synechocystis PCC 6803.

  2007cited by this paper
• Bioinformatics and Computational Biology Solutions Using R and Bioconductor

  2007cited by this paper
• Cyanobacterial Small Chlorophyll-binding Protein ScpD (HliB) Is Located on the Periphery of Photosystem II in the Vicinity of PsbH and CP47 Subunits*

  2006cited by this paper
• Serine/Threonine Protein Kinase SpkA in Synechocystis sp. Strain PCC 6803 Is a Regulator of Expression of Three Putative pilA Operons, Formation of Thick Pili, and Cell Motility

  2006cited by this paper
• limma: Linear Models for Microarray Data

  2005cited by this paper
• OLIN: optimized normalization, visualization and quality testing of two-channel microarray data

  2005cited by this paper
• Identification of Low-temperature-regulated ORFs in the cyanobacterium Anabaena sp. strain PCC 7120: distinguishing the effects of low temperature from the effects of photosystem II excitation pressure.

  2005cited by this paper
• PsbQ (Sll1638) in Synechocystis sp. PCC 6803 is required for photosystem II activity in specific mutants and in nutrient-limiting conditions.

  2005cited by this paper
• The FtsH protease is required for the repair of Photosystem II in the cyanbacterium Synechocystis 6803 damaged UV-B radiation

  2005cited by this paper
• Consequences of a Deletion in dspA on Transcript Accumulation in Synechocystis sp. Strain PCC6803

  2004cited by this paper
• Open source clustering software.

  2004cited by this paper
• GeneXplorer: an interactive web application for microarray data visualization and analysis

  2004cited by this paper
• Five Histidine Kinases Perceive Osmotic Stress and Regulate Distinct Sets of Genes in Synechocystis*

  2004cited by this paper
• Java Treeview - extensible visualization of microarray data

  2004cited by this paper
• The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategy

  2003cited by this paper
• FtsH Is Involved in the Early Stages of Repair of Photosystem II in Synechocystis sp PCC 6803 Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012609.

  2003cited by this paper
• nblS, a Gene Involved in Controlling Photosynthesis-Related Gene Expression during High Light and Nutrient Stress inSynechococcus elongatus PCC 7942

  2002cited by this paper
• DNA Microarray Analysis of Cyanobacterial Gene Expression during Acclimation to High Light

  2001cited by this paper
• Two distinct mechanisms regulate the transcription of photosystem II genes in Synechocystis sp. PCC 6803.

  2001cited by this paper
• Expression of two nblA-homologous genes is required for phycobilisome degradation in nitrogen-starved Synechocystis sp. PCC6803.

  2001cited by this paper
• Characterization of purified His-tagged CP47-containing photosystem II complexes from a cyanobacterium, Synechocystis sp. PCC 6803

  2001cited by this paper
• CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803

  1998cited by this paper
• Activation of the silent psbA1 gene in the cyanobacterium Synechocystis sp strain 6803 produces a novel and functional D1 protein.

  1997cited by this paper
• The heme oxygenase gene (pbsA) in the red alga Rhodella violacea is discontinuous and transcriptionally activated during iron limitation.

  1997cited by this paper
• Compilation of all genes encoding bacterial two-component signal transducers in the genome of the cyanobacterium, Synechocystis sp. strain PCC 6803.

  1996cited by this paper
• Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions.

  1996cited by this paper
• Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions (supplement).

  1996cited by this paper
• Turnover of the D1 protein and of Photosystem II in a Synechocystis 6803 mutant lacking Tyrz

  1995cited by this paper
• Photoinhibition of Photosystem II. Inactivation, protein damage and turnover.

  1993cited by this paper
• Differential expression of the psbA genes in the cyanobacterium Synechocystis 6803

  1993cited by this paper
• Influence of light on accumulation of photosynthesis-specific transcripts in the cyanobacterium Synechocystis 6803

  1989cited by this paper

• Isolation of a Novel Streptomyces sp. TH05 with Potent Cyanocidal Effects on Microcystis aeruginosa

  2025cites this paper
• Advancements in photosynthetic efficiency: Pathways, regulation, and biotechnological applications for enhancing crop productivity

  2025cites this paper
• CurT/CURT1 proteins are involved in cell and chloroplast division coordination of cyanobacteria and green algae

  2025cites this paper
• Low-temperature-induced stress activates lipid deacylation at the sn-1 position in the cyanobacterium Synechocystis sp. PCC 6803.

  2025cites this paper
• Inhibition mechanisms of perchlorate on the photosynthesis of cyanobacterium Synechocystis sp. PCC6803: Insights from physiology and transcriptome analysis.

  2024cites this paper
• Interactors and effects of overexpressing YlxR/RnpM, a conserved RNA binding protein in cyanobacteria

  2024cites this paper
• Navigating the microalgal maze: a comprehensive review of recent advances and future perspectives in biological networks

  2024cites this paper
• Study of excess manganese stress response highlights the central role of manganese exporter Mnx for holding manganese homeostasis in the cyanobacterium Synechocystis sp. PCC 6803

  2024cites this paper
• Investigation of singlet-oxygen-responsive genes in the cyanobacterium Synechocystis PCC 6803.

  2024cites this paper
• Phylogenetic Profiling Analysis of the Phycobilisome Revealed a Novel State-Transition Regulator Gene in Synechocystis sp. PCC 6803

  2024cites this paper
• Customized molecular tools to strengthen metabolic engineering of cyanobacteria

  2024cites this paper
• Spatial Proteome Reorganization of a Photosynthetic Model Cyanobacterium in Response to Abiotic Stresses.

  2023cites this paper
• The volatilome reveals microcystin concentration, microbial composition, and oxidative stress in a critical Oregon freshwater lake

  2023cites this paper
• A hundred spotlights on microbiology: how microorganisms shape our lives

  2022cites this paper
• Functional annotation and evaluation of hypothetical proteins in cyanobacterium Synechocystis sp. PCC 6803

  2022cites this paper
• Different Regulatory Modes of Synechocystis sp. PCC 6803 in Response to Photosynthesis Inhibitory Conditions

  2021cites this paper
• Genome-wide identification and characterization of Fur-binding sites in the cyanobacteria Synechocystis sp. PCC 6803 and PCC 6714

  2021cites this paper
• Thylakoid attachment to the plasma membrane in Synechocystis sp. PCC 6803 requires the AncM protein.

  2021cites this paper
• Rediscovering and repurposing natural microbial macromolecules through computational approaches

  2021cites this paper
• Cycling between growth and production phases increases cyanobacteria bioproduction of lactate.

  2021cites this paper
• Multi-Omic Analyses Reveal Habitat Adaptation of Marine Cyanobacterium Synechocystis sp. PCC 7338

  2021cites this paper
• Minor pilins are involved in motility and natural competence in the cyanobacterium Synechocystis sp. PCC 6803

  2021cites this paper
• The Role of Outer Membrane Protein(s) Harboring SLH/OprB-Domains in Extracellular Vesicles’ Production in Synechocystis sp. PCC 6803

  2021cites this paper
• Deciphering and engineering high-light tolerant cyanobacteria for efficient photosynthetic cell factories

  2020cites this paper
• Modeling a global regulatory network of Methanothermobacter thermautotrophicus strain ∆H

  2020cites this paper
• Database resources for cyanobacterial research

  2020cites this paper
• Bioremediation of agricultural runoff and biopolymers production from cyanobacteria cultured in demonstrative full-scale photobioreactors

  2020cites this paper
• High Light Induced Alka(e)ne Biodegradation for Lipid and Redox Homeostasis in Cyanobacteria

  2020cites this paper
• Graphitic bio-char and bio-oil synthesis via hydrothermal carbonization-co-liquefaction of microalgae biomass (oiled/de-oiled) and multiple heavy metals remediations.

  2020cites this paper
• Putative probiotic cyanobacterium spp from the coastal waters of Cochin polyphasic taxonomy fate of axenic cultures and heterotrophic bacterial associates

  2019cites this paper
• Small-scale phyco-mitigation of raw urban wastewater integrated with biodiesel production and its utilization for aquaculture.

  2019cites this paper
• Building an Inducible T7 RNA Polymerase/T7 Promoter Circuit in Synechocystis sp. PCC6803.

  2019cites this paper
• Thylakoid membrane architecture in cyanobacteria

  2018cites this paper
• Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells1[OPEN]

  2018cites this paper
• Diurnal Changes in Active Carbon and Nitrogen Pathways Along the Temperature Gradient in Porcelana Hot Spring Microbial Mat

  2018cites this paper
• Synthetic Gene Regulation in Cyanobacteria.

  2018cites this paper
• Systems and synthetic biology for the biotechnological application of cyanobacteria.

  2018cites this paper
• Analysis of the light intensity dependence of the growth of Synechocystis and of the light distribution in a photobioreactor energized by 635 nm light

  2018cites this paper
• Far‐red light promotes biofilm formation in the cyanobacterium Acaryochloris marina

  2018cites this paper
• Translating Divergent Environmental Stresses into a Common Proteome Response through the Histidine Kinase 33 (Hik33) in a Model Cyanobacterium*

  2017cites this paper
• Association of Psb28 and Psb27 Proteins with PSII-PSI Supercomplexes upon Exposure of Synechocystis sp. PCC 6803 to High Light.

  2017cites this paper
• Vers la reprogrammation métabolique de la cyanobactérie modèle Synechocystis pour la production durable de biocarburants : structuration des flux du carbone par CP12 et implications sur l’équilibre bioénergétique, l’hydrogénase et l’intégrité génomique

  2017influential citation
• Translating Divergent Environmental Stresses into a Common Proteome Response through Hik33 in a Model Cyanobacterium.

  2017cites this paper
• Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803

  2017cites this paper
• Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

  2016cites this paper
• Thylakoid Membrane Architecture in Synechocystis Depends on CurT, a Homolog of the Granal CURVATURE THYLAKOID1 Proteins

  2016influential citation
• The Cyanobacterial Ribosomal-Associated Protein LrtA Is Involved in Post-Stress Survival in Synechocystis sp. PCC 6803

  2016cites this paper
• The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels

  2016cites this paper
• CyanoBase: a large-scale update on its 20th anniversary

  2016cites this paper
• POLITECNICO DI TORINO Repository ISTITUZIONALE Analysis of the light intensity dependence of the growth of Synechocystis and of the light distribution in a photobioreactor energized by 635 nm light /

  year unknowncites this paper
• Identification of the direct regulon of NtcA during early Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 Synechocystis sp. PCC 6803

  year unknowncites this paper