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Gene regulation in cyanobacteria


Taina Tyystjärvi
e-mail: taityy [at]
tel. +358 2 3335797


Taina Tyystjärvi, Ph .D, Lecturer, Project Leader
Juha Kurkela, PhD Student
Satu Koskinen, Researcher
Cyanobacteria are responsible of at least one third of carbon fixation on the Earth and thus they are important primary producers. In addition, some species are capable of nitrogen fixation. Acclimation of cyanobacteria to changing environmental conditions requires adjustment of gene expression. The sigma subunit of RNA polymerase has a central role in regulating gene expression in cyanobacteria. The sigma subunit is required for transcription initiation and it recognizes promoter regions. Cyanobacteria have one essential sigma factor and varying numbers of other sigma subunits. Replacement of one sigma subunit in the RNA polymerase by another one induces a main change in the gene expression profile.


The principal sigma factor of the cyanobacterium Synechochystis sp. PCC 6803 is a SigA factor. Four sigma factors, SigB, SigC, SigD and SigE, closely resemble the SigA factor. These sigma factors are not essential under optimal conditions but recent results have revealed that they are important under different stress conditions. We aim at elucidation of the signalling cascades for each sigma factor and at finding out what genes and how each sigma factor regulates. Simultaneously, our results reveal signalling cascades participating in acclimation processes under different stress conditions. We use both molecular biology methods and biochemical and biophysical methods in our research.


This basic research will help us to understand how ecologically important cyanobacteria acclimate to environmental changes. Furthermore, understanding of cyanobacterial gene regulation is crucial for any project aiming at using cyanobacteria as biofactories to produce useful compounds like bioenergy products.


Stensjö K, Vavitsas K, Tyystjärvi T. (2017) Harnessing transcription for bioproduction in cyanobacteria. Physiologia Plantarum. [A2]  (Epub ahead of print)
Kurkela, J., Hakkila, K., Antal*, T. & Tyystjarvi, T. 2017:  Acclimation to high CO2 requires the ω subunit of the RNA polymerase in Synechocystis. PLANT PHYSIOLOGY  174(1):172-184  (Epub 2017 Mar 28).
Antal, TK.; Kurkela, J.; Parikainen, M.; Kårlund, A.; Hakkila, K.; Tyystjärvi, E. & Tyystjärvi, T. 2016:  Roles of group 2 sigma factors in acclimation of the cyanobacterium Synechocystis sp. PCC 6803 to nitrogen deficiency. - Plant Cell Physiol. 57(6):1309-18.   Free article   (Epub 2016 Apr 19).
Rantamäki, S.; Meriluoto*, J.; Spoof*, L.; Puputti, EM.; Tyystjärvi, T. & Tyystjärvi, E. 2016: Oxygen produced by cyanobacteria in simulated Archaean conditions partly oxidizes ferrous iron but mostly escapes-conclusions about early evolution. - Photosynth Res. 130(1-3):103-111.   (Epub 2016 Feb 19).
Koskinen, S.; Hakkila, K.; Gunnelius, L.; Kurkela, J.; Wada*, H. & Tyystjärvi, T. 2016:  In vivo recruitment analysis and a mutant strain without any group 2 σ factor reveal roles of different σ factors in cyanobacteria. - MOLECULAR MICROBIOL:OGY 99(1): 43-54.   (Epub 2015 Sep 10).
Gunnelius, L.; Kurkela, J.; Hakkila, K.; Koskinen, S.; Parikainen, M. & Tyystjärvi, T. 2014:  The ω subunit of RNA polymerase is essential for thermal acclimation of the cyanobacterium Synechocystis Sp. PCC 6803. - PLoS One 9(11): e112599.   (Epub 2014 Nov 11).
Gunnelius, L.; Hakkila, K.: Kurkela, J.; Wada*, H.; Tyystjärvi, E. & Tyystjärvi, T. 2014:  The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria. - NUCLEIC ACIDS RESEARCH 42(7): 4606-4614.   Free article   (Epub 2014 Jan 29).
Hakkila, K.; Antal, T.; Rehman*, AU.; Kurkela, J.; Wada*, H.; Vass*, I.; Tyystjärvi, E. & Tyystjärvi, T. 2014:  Oxidative stress and photoinhibition can be separated in the cyanobacterium Synechocystis sp. PCC 6803. - BIOCHIMICA ET BIOPHYSICA ACTA - BIOENERGETICS 1837(2): 217-225.   (Epub 2013 Nov 22)
Hakkila, K.; Antal, T.; Gunnelius, L.; Kurkela, J:; Matthijs*, HC.; Tyystjärvi, E. & Tyystjärvi, T. 2013: Group 2 sigma factor mutant ΔsigCDE of the cyanobacterium Synechocystis sp. PCC 6803 reveals functionality of both carotenoids and flavodiiron proteins in photoprotection of photosystem II. -  PLANT & CELL PHYSIOLOGY 54(11): 1780-1790.
Tyystjärvi T, Huokko T, Rantamäki S, Tyystjärvi E (2013) Impact of different group 2 sigma factors on light use efficiency and high salt stress in the cyanobacterium Synechocystis sp. PCC 6803. PloS ONE 8(4):e63020.
Antal T, Harju E, Pihlgren L, Lastusaari M, Tyystjärvi T, Hölsä J, Tyystjärvi E (2012): Use of near-infrared radiation for oxygenic photosynthesis via photon up-conversion. International Journal of Hydrogen Energy 37: 8859-8863.
Nikkinen H-L, Hakkila K, Gunnelius L, Huokko T, Pollari M, Tyystjärvi T (2012): The SigB σ factor regulates multiple salt acclimation responses of the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiology 158: 514-523.
Hakala-Yatkin M, Sarvikas P, Paturi P, Mäntysaari M, Mattila H, Tyystjärvi T, Nedbal L,  Tyystjärvi E (2011): Magnetic field protects plants against high light by slowing down production of singlet oxygen. Physiologia Plantarum 142:26-34.
Pollari M, Rantamäki S, Huokko T, Kårlund-Marttila A, Virjamo V, Tyystjärvi E, Tyystjärvi T (2011): Effects of deficiency and overdose of group 2 sigma factors in triple inactivation strains of Synechocystis sp. PCC strain 6803. Journal of Bacteriology 193: 265-273.
Antal T, Mattila H, Hakala-Yatkin M, Tyystjärvi T, Tyystjärvi E (2010):  Acclimation of photosynthesis to nitrogen deficiency in Phaseolus vulgaris.  Planta 232: 887-898.
Sarvikas P, Tyystjärvi T, Tyystjärvi E (2010):  Kinetics of prolonged photoinhibition revisited: Photoinhibited photosystem II centres do not protect the active ones against loss of oxygen evolution.  Photosynthesis Research 103:7-17.
Gunnelius L, Tuominen I, Rantamäki S, Pollari M, Ruotsalainen V, Tyystjärvi E and Tyystjärvi T (2010): SigC sigma factor is involved in acclimation to low inorganic carbon at high temperature in Synechocystis sp. PCC 6803. Microbiology 156: 220-229.
Pollari M, Ruotsalainen V, Rantamäki S, Tyystjärvi E and Tyystjärvi T (2009) Simultaneous inactivation of sigma factors B and D interferes with light acclimation of the cyanobacterium Synechocystis sp. strain PCC 6803. Journal of Bacteriology 12: 3992-4001.
Pollari M, Gunnelius L, Tuominen I, Ruotsalainen V, Tyystjärvi E, Salminen T and Tyystjärvi T (2008) Characterization of single and double inactivation strains reveals new physiological roles for group 2 sigma factors in the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiology 147: 1994-2005
Tuominen I, Pollari M, von Wobeser EA, Tyystjärvi E, Ibelings BW, Matthijs HCP and Tyystjärvi T (2008) Sigma factor SigC is required for heat acclimation of the cyanobacterium Synechocystis sp. strain PCC 6803. FEBS Letters 582: 346-350
Pollari M and Tyystjärvi T (2008) The SigB sigma factor of the cyanobacterium Synechocystis sp. PCC 6803 is necessary for adaptation to high-salt stress. - In: Photosynthesis. Energy from the Sun. 14th International Congress on Photosynthesis Research, Glasgow 22-27 July 2007. Allen, J.F., Gantt, E., Golbeck, J.H., Osmond, B. (eds.). Springer, Heidelberg, ISBN: 978-1-4020-6707-5.
Tuominen I, Pollari M, Tyystjärvi E and Tyystjärvi T (2006) The SigB sigma factor is involved in high temperature responses in the cyanobacterium Synechocystis sp. PCC6803. FEBS Letters 580: 319-323.
Sarvikas P, Hakala M, Pätsikkä E, Tyystjärvi T, Tyystjärvi E (2006) Action spectrum of photoinhibition in leaves of npq1-2 and npq4-1 mutant of Arabidopsis thaliana. Plant and Cell Physiology 47: 391-400.
Hakala M, Rantamäki S, Puputti E-M, Tyystjärvi T, Tyystjärvi E (2006) Photoinhibiotion of manganase enzymes: insights into the mechanism of photosystem II photoinhibition. Journal of Experimental Botany 57: 1809-1816.

Hakala M, Tuominen I, Keränen M, Tyystjärvi T, Tyystjärvi E (2005) Evidence for the role of the oxygen-evolving manganese complex in photoinhibition of Photosystem II. Biochemica et  Biophysica Acta 1706: 68-80.

Herranen M, Tyystjärvi T, Aro E-M (2005) Regulation of photosystem I reaction center genes in Synechcystis sp. strain PCC6803 during light acclimation. Plant and Cell Physiology 46: 1484-1493.

Tyystjärvi T, Sirpiö S,  Aro E-M (2004) Post-transcriptional regulation of psbA gene family in the cyanobacterium Synechococcus sp. PCC 7942. FEBS Letters 576: 211-215. 
Tuominen I, Tyystjärvi E and Tyystjärvi T (2003) Expression of primary sigma factor (PSF) and PSF-like sigma factors in the cyanobacterium Synechocystis sp. strain PCC 6803. Journal of Bacteriology 185: 1116-1119
Sakurai I, Hagio M, Gombos Z, Tyystjarvi T, Paakkarinen V, Aro E-M, Wada H (2003) Requirement of Phosphatidylglycerol for Maintenance of Photosynthetic Machinery. Plant Physiology 133: 1376-1384.

Mulo P, Pursiheimo S, Hou C-X, Tyystjärvi T, Aro E-M (2003) Multiple effects of antibiotics on chloroplast and nuclear gene expression. Functional Plant Biology 30: 1097-1103.

Tyystjärvi T, Tuominen I, Herranen M, Aro E-M, Tyystjärvi E (2002) Action spectrum of psbA gene transcription is similar to that of photoinhibition in Synechocystis sp. PCC 6803. FEBS Letters 516: 167-171

Guiamét J,  Tyystjärvi E, Tyystjärvi T, John I, Kairavuo M, Pichersky E and  Noodén L (2002) Photoinhibition and loss of photosystem II center proteins during senescence of soybean leaves.  Enhancement of photoinhibition by the stay-green mutation cytG. Physiologia Plantarum 115: 468-478

Tyystjärvi T, Herranen M, Aro E-M (2001) Regulation of translation elongation in cyanobacteria: membrane targeting of the ribosome nascent chain complexes controls the synthesis of D1 protein. Molecular Microbiology 40: 476-484

Herranen M, Aro E-M, Tyystjärvi T (2001) Two distinct mechanisms regulate the transcription of Photosystem II genes in Synechocystis sp. PCC 6803. Physiologia Plantarum 112: 531-539.

Tyystjärvi T, Tyystjärvi E, Ohad I, Aro E-M (1998) Exposure of Synechocystis 6803 cells to series of single turnover flashes increases the psbA transcript level by activating transcription and down-regulating psbA mRNA degradation. FEBS Letters 436: 483-487

Mulo P, Tyystjärvi T, Tyystjärvi E, Govindjee, Mäenpää P and Aro E-M (1997) Mutagenesis of the D-E loop of photosystem II reaction centre protein D1. Function and assembly of photosystem II.  Plant Molecular Biology 33: 1059-1071

Salih G, Wiklund R, Tyystjärvi T, Mäenpää P, Gerez C and Jansson C (1996) Constructed deletions in lumen-exposed regions of the D1 protein the cyanobacterium Synechocystis 6803: Effects on D1 insertion and accumulation in the thylakoid membrane and on photosystem II assembly. Photosynthesis Research 49: 131-140

Tyystjärvi T, Mulo P, Mäenpää P and Aro E-M (1996) D1 polypeptide degradation may regulate psbA gene expression at transcriptional and translational levels in Synechocystis sp. PCC 6803. Photosynthesis Research 47: 111-120

Mäenpää P, Miranda T, Tyystjärvi E, Tyystjärvi T, Govindjee, Ducruet J-M, Etienne A-L and Kirilovsky D (1995) A mutation in the D-de loop of D1 modifies the stability of the S2QA- and  S2QB- states in Photosystem II. Plant Physiology 107: 187-197.

Tyystjärvi T, Aro E-M, Jansson C and Mäenpää P (1994) Changes of amino acid sequence in PEST-like area and QEEET motif affect degradation rate of D1 polypeptide in photosystem II. Plant Molecular Biology 25: 517-526.
Mäenpää P, Kallio T, Mulo P, Salih GF, Aro E-M, Tyystjärvi E and Jansson C (1993) Site-specific mutations in the D1 polypeptide affect the susceptibility of Synechocystis 6803 cells to photoinhibition. Plant Molecular Biology 22: 1-12.