Deciphering the gene regulatory networks of cyanobacteria
FCT Investigator Developmental Grant, Portugal: IF/00881/2013


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. The objective of this project was the derivation and validation of detailed models of gene regulatory networks in cyanobacteria. To cope with their complexity, experimental and computational approaches including next-generation sequencing and in silico reverse engineering are combined. As model system, we have been using Synechocystis PCC6803, for which adequate methods and resources have been established in the SysBioLab. A special focus was put on interconnections between transcriptional regulation, metabolism and photosynthesis, as they can serve as the basis for rational re-engineering of cyanobacteria using tools of synthetic biology with potential application such the production of bio-energy or high-value components.

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.


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)


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