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Mustila H, Paananen P, Battchikova N, Santana-Sánchez A, Muth-Pawlak D, Hagemann M, Aro EM, Allahverdiyeva Y. The Flavodiiron Protein Flv3 Functions as a Homo-Oligomer During Stress Acclimation and is Distinct from the Flv1/Flv3 Hetero-Oligomer Specific to the O2 Photoreduction Pathway. PLANT & CELL PHYSIOLOGY 2016; 57:1468-1483. [PMID: 26936793 PMCID: PMC4937785 DOI: 10.1093/pcp/pcw047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/23/2016] [Indexed: 05/06/2023]
Abstract
The flavodiiron proteins (FDPs) Flv1 and Flv3 in cyanobacteria function in photoreduction of O2 to H2O, without concomitant formation of reactive oxygen species, known as the Mehler-like reaction. Both Flv1 and Flv3 are essential for growth under fluctuating light (FL) intensities, providing protection for PSI. Here we compared the global transcript profiles of the wild type (WT), Δflv1 and Δflv1/Δflv3 grown under constant light (GL) and FL. In the WT, FL induced the largest down-regulation in transcripts involved in carbon-concentrating mechanisms (CCMs), while those of the nitrogen assimilation pathways increased as compared with GL. Already under GL the Δflv1/Δflv3 double mutant demonstrated a partial down-regulation of transcripts for CCM and nitrogen metabolism, while in FL conditions the transcripts for nitrogen assimilation were strongly down-regulated. Many alterations were specific only for Δflv1/Δflv3, and not detected in Δflv1, suggesting that certain transcripts are affected primarily because of the lack of flv3 By constructing the strains overproducing solely either Flv1 or Flv3, we demonstrate that the homo-oligomers of these proteins also function in acclimation of cells to FL, by catalyzing reactions with as yet unidentified components, while the presence of both Flv1 and Flv3 is a prerequisite for the Mehler-like reaction and thus the electron transfer to O2 Considering the low expression of flv1, it is unlikely that the Flv1 homo-oligomer is present in the WT.
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Affiliation(s)
- Henna Mustila
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Pasi Paananen
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Natalia Battchikova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Anita Santana-Sánchez
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Dorota Muth-Pawlak
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Martin Hagemann
- Institut Biowissenschaften, Pflanzenphysiologie, Universität Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Eva-Mari Aro
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Yagut Allahverdiyeva
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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Klähn S, Orf I, Schwarz D, Matthiessen JKF, Kopka J, Hess WR, Hagemann M. Integrated Transcriptomic and Metabolomic Characterization of the Low-Carbon Response Using an ndhR Mutant of Synechocystis sp. PCC 6803. PLANT PHYSIOLOGY 2015; 169:1540-56. [PMID: 25630438 PMCID: PMC4634042 DOI: 10.1104/pp.114.254045] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/27/2015] [Indexed: 05/17/2023]
Abstract
The acquisition and assimilation of inorganic carbon (Ci) represents the largest flux of inorganic matter in photosynthetic organisms; hence, this process is tightly regulated. We examined the Ci-dependent transcriptional and metabolic regulation in wild-type Synechocystis sp. PCC 6803 compared with a mutant defective in the main transcriptional repressor for Ci acquisition genes, the NAD(P)H dehydrogenase transcriptional regulator NdhR. The analysis revealed that many protein-coding transcripts that are normally repressed in the presence of high CO2 (HC) concentrations were strongly expressed in ∆ndhR, whereas other messenger RNAs were strongly down-regulated in mutant cells, suggesting a potential activating role for NdhR. A conserved NdhR-binding motif was identified in the promoters of derepressed genes. Interestingly, the expression of some NdhR-regulated genes remained further inducible under low-CO2 conditions, indicating the involvement of additional NdhR-independent Ci-regulatory mechanisms. Intriguingly, we also observed that the abundance of 52 antisense RNAs and 34 potential noncoding RNAs was affected by Ci supply, although most of these molecules were not regulated through NdhR. Thus, antisense and noncoding RNAs could contribute to NdhR-independent carbon regulation. In contrast to the transcriptome, the metabolome in ∆ndhR cells was similar to that of wild-type cells under HC conditions. This observation and the delayed metabolic responses to the low-CO2 shift in ∆ndhR, specifically the lack of transient increases in the photorespiratory pathway intermediates 2-phosphoglycolate, glycolate, and glycine, suggest that the deregulation of gene expression in the ΔndhR mutant successfully preacclimates cyanobacterial cells to lowered Ci supply under HC conditions.
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Affiliation(s)
- Stephan Klähn
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Isabel Orf
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Doreen Schwarz
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Jasper K F Matthiessen
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Joachim Kopka
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Martin Hagemann
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
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