Ing. Roman Sobotka, PhD.

Laboratory Head

Roman Sobotka

 

Biosyntesis and function of photosynthetic pigments (R. Sobotka)

Algatech Centre, Institute of Microbiology, Opatovický mlýn, Třeboň, Phone: +420 384340491, E-mail: sobotka@alga.cz

Citizenship

Czech Republic

Higher education

  • MSc, Plant breeding and genetic engineering, Faculty of Agriculture, University of South Bohemia, České Budějovice, Czech Republic (Jun 1997)
  • PhD, Plant genetics, Faculty of Agriculture, University of South Bohemia, České Budějovice, Czech Republic (Jul 2001)

Employment history and stays abroud

2002

Compulsory military service

2003-2006

Post-doc position, Dr. Martin Tichy' group, Institute of Microbiology, Třeboň, Czech Republic

Oct 2006 - Dec 2007

FEMS fellowship and research assistant, Laboratory of Prof. Neil Hunter, Department of Molecular Biology and Biotechnology, University of Sheffield (UK).

2008 -now

Scientist, Laboratory of Photosynthesis, Institute of Microbiology, Třeboň, Czech Republic

2008-2012

3x1 months on University of Sheffield, short-term stays (University of Giessen; Biological Reseach Center, Szeged)

2013

3 months on Imperial College, London; one week on Nanyang University, Singapore

Research interests:

To elucidate how chlorophyll is made inside of the cell, how chlorophyll biosynthesis is regulated, what way chlorophylls are built into photosynthetic complexes and what is the fate of this pigment once these complexes are degraded

Invited lectures and conference talks:

Tetrapyrrole Photoreceptors of Photosynthetic Organisms (ICTPPO), Migal, Israel, 2015
Plastid Preview, University of Greenwich, 2013
The Tetrapyrrole Discussion Group, Canterbury, 2013
University of Tubingen, 2013
Tetrapyrrole Gordon Conference, Newport, 2012
University of Copenhagen, 2010
Kongres ČSSM, Stara Lesna, 2010
Conference on Tetrapyrrole Photoreceptors of Photosynthetic Organisms, Asilomar, 2009
Photosynthesis Gordon Conference, Boston, 2008
European Workshop on The Molecular Biology of Cyanobacteria, Ceske Budejovice, 2008
Humboldt University, Berlin, 2007

 

Selected publications (since 2005)

Kopečná J, Cabeza de Vaca I, Adams NBP, Davison PA, Brindley AA, Hunter, CN, Guallar V, Sobotka
R. (2015) Porphyrin binding to Gun4 protein, facilitated by a flexible loop, controls metabolite flow
through the chlorophyll biosynthetic pathway. J. Biol. Chem. 290, 28477–28488,

Kopečná J, Pilný J, Krynická V, Tomčala A, Kis M, Gombos Z, Komenda J, Sobotka R. (2015) Lack of
phosphatidylglycerol inhibits chlorophyll biosynthesis at multiple sites and limits chlorophyllide
reutilization in Synechocystis sp. strain PCC 6803. Plant Physiol. 169, 1307–1317

Staleva H, Komenda J, Shukla MK, Šlouf V, Kaňa R, Polívka T, Sobotka R. (2015) Mechanism of
photoprotection in the cyanobacterial ancestor of plant antenna proteins. Nature Chem. Biol. 11,
287‐291

Linhartová M, Bučinská L, Halada P, Ječmen T, Šetlík J, Komenda J, Sobotka R. (2014) Accumulation
of the Type IV prepilin triggers degradation of SecY and YidC and inhibits synthesis of Photosystem II
proteins in the cyanobacterium Synechocystis PCC 6803. Mol. Microbiol. 93:1207‐23.

Knoppová J, Sobotka R, Tichý M, Yu J, Koník P, Halada P, Nixon PJ, Komenda J. (2014) Identification of
a novel chlorophyll‐binding protein complex involved in the early steps of photosystem two
assembly. Plant Cell 26:1200‐12.

Chidgey JW, Linhartová M, Komenda J, Jackson PJ, Dickman MJ, Canniffe DP, Koník P, Pilný J, Hunter
CN, Sobotka R. (2014) A cyanobacterial chlorophyll synthase‐HliD complex associates with the Ycf39
Protein and the YidC/Alb3 Insertase. Plant Cell 26:1267‐79.

Sobotka R. (2013) Making proteins green; biosynthesis of chlorophyll‐binding proteins in
cyanobacteria. Photosynth Res. 119:223‐32

Kopečná J, Sobotka R, Komenda J. (2013) Inhibition of chlorophyll biosynthesis at the
protochlorophyllide reduction step results in the parallel depletion of Photosystem I and
Photosystem II in the cyanobacterium Synechocystis PCC 6803. Planta 160:2239‐50

Kopečná J, Komenda J, Bučinská L, Sobotka R. (2012) Long‐term acclimation of the cyanobacterium
Synechocystis PCC 6803 to high light is accompanied by an enhanced production of chlorophyll that
is preferentially channeled to trimeric PSI. Plant Physiol. 160:2239‐50.

Hollingshead S, Kopečná J, Jackson PJ, Canniffe DP, Davison PA, Dickman MJ, Sobotka R, Hunter CN.
(2012) Conserved chloroplast open‐reading frame ycf54 is required for activity of the magnesiumprotoporphyrin
monomethylester oxidative cyclase in Synechocystis PCC 6803. J. Biol. Chem.
287:27823‐33.

Wallner T, Hagiwara Y, Bernát G, Sobotka R, Reijerse EJ, Frankenberg‐Dinkel N, Wilde A. (2012)
Inactivation of the conserved open reading frame ycf34 of Synechocystis sp. PCC 6803 interferes with
the photosynthetic electron transport chain. BBA ‐ Bioenergetics, 1817:2016‐26.

Komenda J, Sobotka R, Nixon PJ. (2012) Assembling and maintaining the Photosystem II complex in
chloroplasts and cyanobacteria. Curr Opin Plant Biol. 15:245–251.

Kořený, L. Sobotka, R. Kovářová, J. Gnipová, A. Flegontov, P. Horváth, A. Oborník, M. Ayala, FJ. Lukeš,
J. (2012) Aerobic kinetoplastid flagellate Phytomonas does not require heme for viability. PNAS
109:3808‐13.

Kaňa, R. Kotabová, E. Sobotka, R. Prášil, O. (2012) Non‐photochemical quenching in cryprohyte alga
Rhodomonas salina is located in chlorophyll a/c antennae. PLoS ONE 7:e29700.

Komenda, J. Knoppova, J. Kopečná, J. Sobotka, R. Halada, P. Yu, J. Nickelsen, J. Boehm, M. Nixon, PJ.
(2012) The Psb27 assembly factor binds to the CP43 complex of Photosystem II in the
cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol. 158, 476‐486.

Kořený, L, Sobotka, R, Janouškovec, J, Keeling, PJ, Obornik, M. (2011) Tetrapyrrole synthesis of
photosynthetic chromerids is likely homologous to the unusual pathway of apicomplexan parasites.
Plant Cell, 23:3454‐62.

Sobotka R, Tichý M, Wilde A, Hunter CN. (2011) Functional assignments for the C‐terminal domains
of the ferrochelatase from Synechocystis PCC 6803: the CAB domain plays a regulatory role and
region II is essential for catalysis. Plant Physiol. 155:1735‐47.

Dobáková M, Sobotka R, Tichý M, Komenda J. (2009) The Psb28 protein is involved in the
biogenesis of the photosystem II inner antenna CP47 (PsbB) in the cyanobacterium
Synechocystis sp. PCC 6803. Plant Physiol. 149:1076‐86.

Sobotka R, Dühring U, Komenda J, Peter E, Gardian Z, Tichy M, Grimm B, Wilde A. (2008)
Importance of the cyanobacterial Gun4 protein for chlorophyll metabolism and assembly of
photosynthetic complexes. J. Biol. Chem. 283: 25794‐802.

Sobotka R, McLean S, Žuberová M, Hunter CN, Tichý M. (2008) The C‐terminal extension of
ferrochelatase is critical for enzyme activity and for functioning of the tetrapyrrole pathway in
Synechocystis strain PCC 6803. J. Bacteriol. 190: 2086‐95.

Sobotka R, Komenda J, Bumba L, Tichý M. (2005) Photosystem II assembly in CP47 mutant of
Synechocystis sp. PCC 6803 is dependent on the level of chlorophyll precursors regulated by
ferrochelatase. J. Biol. Chem. 280: 31595‐31602.