The regulation of photosynthesis in cyanobacteria: A systems biology approach


Life depends on the conversion of sunlight to chemical energy by photosynthesis. We now know in great detail the structure and functions of the main components of photosynthesis, from the absorption of light particles by protein-pigment binding complexes to the assimilation of inorganic carbon (CO2) into carbohydrates by the Calvin-Benson cycle. However, our knowledge of photosynthesis regulation at cellular level is still in its infancy.

To increase our understanding of photosynthesis, we seek to elucidate its molecular regulation and coordination with other processes through an innovative genomic approach complemented by integrative computational analyses at the systems level. Using such combined approach, we aim to to determine the structure and functionality of the regulatory molecular networks interconnecting photosynthesis with downstream processes such as glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway.

For this project, we chose a well-established model system in the study of photosynthesis: the cyanobacterium Synechocystis sp. PCC6803. Despite extensive studies of photosynthesis in Synechocystis, little is currently known about its regulation. The establishment of the CyanoEXpress database, which presents the most comprehensive collection of transcriptome data for Synechocystis to date, enabled us to carry out a systems-level analysis of the adaptive response of photosynethesis to various environmental changes (Scientific Reports, 2016). To gain specific insights into the regulation of photosynethetic genes and their coordination with other processes, we also examined the regulation imposed by key global transcription factors (TFs) that occupy central positions in the coordination between photosynthesis and downstream pathways. To study these regulators, we used a combination of state of the art experimental and analytical techniques. Potential target genes will be identified by combining different next generation sequencing technology (ChIP- & RNA-Seq) and computational TF binding site prediction. To critically assess our experimental results and to gain new insights at a systems level, models of the regulatory molecular network underlying the photosynthetic processes will be reconstructed in silico using a combination of our newly generated and existing data. Such network models will provide us with powerful tool to study how the transcriptional regulation is carried out and coordinated on a systems level, and, and to establish Synechocystis as a photosynthetic model organism for systems and synthetic biology (Frontiers in Genomics, 2015).

Project Team

Databases & Software


In this project, we have continued to integrate additional transcriptome profiles in our CyanoEXpress database. Notably, the new version of CyanoEXpress also includes expression profiles for non-coding genes, which play important roles in the regulation of gene expression. Moreover, we have implemented new features enhancing the capacity of CyanoEXpress to reveal regulatory patterns in expression data.


Matthias Riediger, Miguel A. Hernández-Prieto, Kuo Song, Wolfgang R. Hess and Matthias E. Futschik (2021) Genome-wide identification and characterization of Fur binding sites in the cyanobacterium Synechocystis sp. PCC 6803. DNA Research, 28, (6): dsab023 (pdf+html)

Joaquín Giner-Lamia, Miguel A. Hernández-Prieto, and Matthias E. Futschik (2018) ChIP-seq Experiment and Data Analysis in the Cyanobacterium Synechocystis sp. PCC 6803. Bio-protocol 8(12): e2895 (pdf+html)

Joaquín Giner-Lamia, Rocio Robles-Rengel, Miguel A. Hernández-Prieto, M. Isabel Muro-Pastor, Francisco J. Florencio, and Matthias E. Futschik (2017) Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803, Nucleic Acids Research 45: 11800 - 11820 (pdf+html)

p>Jens Georg, Gergana Kostova , Linda Vuorijoki, Verena Schön, Taro Kadowaki, Tuomas Huokko, Desirée Baumgartner, Maximilian Müller, Stephan Klähn, Yagut Allahverdiyeva , Yukako Hihara, Matthias E. Futschik, Eva-Mari Aro, Wolfgang R. Hess (2017) Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1, Current Biology 27(10): 1425-1436 (pdf+html)

Joaquín Giner-Lamia, Sara B. Pereira, Miquel Bovea-Marco, Matthias E. Futschik, Paula Tamagnini, Paulo Oliveira (2016) Extracellular proteins: Novel key components of metal homeostasis in cyanobacteria? Frontiers in Microbiology 7:878 (pdf+html)

Miguel Hernández-Prieto , Trudi Semeniuk , Joaquin Giner-Lamia and Matthias Futschik (2016) The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803, Scientific Reports 6:22168 (pdf + html)

Shany Doron, Ayalla Fedida, Miguel A Hernández-Prieto, Gazalah Sabehi, Iris Karunker, Damir Stazic, Roi Feingersch, Claudia Steglich, Matthias Futschik, Debbie Lindell and Rotem Sorek (2016) Transcriptome dynamics of a broad host-range cyanophage and its hosts. The ISME Journal 10, 1437-1455 (pdf + html)

Miguel A. Hernández-Prieto, Trudi A. Semeniuk and Matthias E. Futschik (2014) Towards a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. Frontiers in Genetics 5:191 (pdf + html)

Miguel Hernandez-Prieto, Ravi Kalathur and Matthias E. Futschik (2014) Molecular networks, their analysis and representation, Chapter 24, 399-418, Springer Handbook of Bio- and Neuroinformatics, ed. Nik Kasabov, Springer (preprint-pdf, Book's web-page)


Miguel A. Hernandez-Prieto, Trudi Semeniuk, Joaquín Giner-Lamia, and Matthias E. Futschik (2018) Transcriptional regulation and coordination of photosynthetic genes in the model cyanobacterium Synechocystis - a comprehensive study based on CyanoEXpress, PHYCONET Annual Conference, London, UK

Matthias Futschik (2018) Deciphering the gene regulatory networks of cyanobacteria, Keynote talk at the 3rd Early Career Researcher Symposium on Cyanobacteria, Freiburg, Germany

Matthias Futschik (2017) Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803, Contributed talk, 10th European Workshop on the Molecular Biology of Cyanobacteria (Abstractbook, Page 35), Cluj-Napoca, Romania

M Futschik, J Giner-Lamia, M Hernandez-Prieto (2016) CyanoEXpress: An interactive web-tool for exploration and visualization of gene expression data from cyanobacteria, NorPlantBio 2016, Trondheim, Norway (abstract)

M Hernandez-Prieto, T Semeniuk, J Giner-Lamia, M Futschik (2016) Transcriptional regulation and coordination of photosynthetic genes in the model cyanobacterium Synechocystis, NorPlantBio 2016, Trondheim, Norway (abstract)

Matthias Futschik, Joaquín Giner-Lamia and Miguel Hernández-Prieto (2015) Transcriptional regulation and coordination of photosynthetic genes in Synechocystis: a comprehensive study based on CyanoEXpress, ISPP 2015, Tübingen, Germany (abstract)

Joaquin Giner-Lamia, Miquel Bovea-Marco, Miguel A. Hernández-Prieto and Matthias E. Futschik (2015) CyanoEXpress: An enhanced tool for on-line analysis and visualization of gene expression data from cyanobacteria, ISPP 2015, Tübingen, Germany (abstract)

Matthias E. Futschik (2013) How Synechocystis adapts to changes in environment: A meta-analysis of its transcriptional responses, Invited Lecture, CyanoFactory Meeting, Porto, Portugal