title: Integrated Analysis of Engineered Carbon Limitation in a Quadruple CO2/HCO3- Uptake Mutant of Synechocystis sp. PCC 6803.
abstract: Cyanobacteria have efficient carbon concentration mechanisms and suppress photorespiration in response to inorganic carbon (Ci) limitation. We studied intracellular Ci limitation in the slow-growing CO2/HCO3 (-)-uptake mutant ΔndhD3 (for NADH dehydrogenase subunit D3)/ndhD4 (for NADH dehydrogenase subunit D4)/cmpA (for bicarbonate transport system substrate-binding protein A)/sbtA (for sodium-dependent bicarbonate transporter A): Δ4 mutant of Synechocystis sp. PCC 6803. When cultivated under high-CO2 conditions, ∆4 phenocopies wild-type metabolic and transcriptomic acclimation responses after the shift from high to low CO2 supply. The ∆4 phenocopy reveals multiple compensation mechanisms and differs from the preacclimation of the transcriptional Ci regulator mutant ∆ndhR (for ndhF3 operon transcriptional regulator). Contrary to the carboxysomeless ∆ccmM (for carbon dioxide concentrating mechanism protein M) mutant, the metabolic photorespiratory burst triggered by shifting to low CO2 is not enhanced in ∆4. However, levels of the photorespiratory intermediates 2-phosphoglycolate and glycine are increased under high CO2. The number of carboxysomes is increased in ∆4 under high-CO2 conditions and appears to be the major contributing factor for the avoidance of photorespiration under intracellular Ci limitation. The ∆4 phenocopy is associated with the deregulation of Ci control, an overreduced cellular state, and limited photooxidative stress. Our data suggest multiple layers of Ci regulation, including inversely regulated modules of antisense RNAs and cognate target messenger RNAs and specific trans-acting small RNAs, such as the posttranscriptional PHOTOSYNTHESIS REGULATORY RNA1 (PsrR1), which shows increased expression in ∆4 and is involved in repressing many photosynthesis genes at the posttranscriptional level. In conclusion, our insights extend the knowledge on the range of compensatory responses of Synechocystis sp. PCC 6803 to intracellular Ci limitation and may become a valuable reference for improving biofuel production in cyanobacteria, in which Ci is channeled off from central metabolism and may thus become a limiting factor.
authors.affiliation: Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.);Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., W.R.H.);Plant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.); andMedical Biology and Electron Microscopy Centre, Medical Faculty, University of Rostock, D-18057 Rostock, Germany (M.F.).
authors.forename: Isabel
authors.identifier: http://orcid.org/0000-0002-7224-9134
authors.initials: I
authors.lastname: Orf
authors.affiliation: Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.);Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., W.R.H.);Plant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.); andMedical Biology and Electron Microscopy Centre, Medical Faculty, University of Rostock, D-18057 Rostock, Germany (M.F.).
authors.forename: Stephan
authors.initials: S
authors.lastname: Klähn
authors.affiliation: Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.);Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., W.R.H.);Plant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.); andMedical Biology and Electron Microscopy Centre, Medical Faculty, University of Rostock, D-18057 Rostock, Germany (M.F.).
authors.forename: Doreen
authors.initials: D
authors.lastname: Schwarz
authors.affiliation: Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.);Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., W.R.H.);Plant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.); andMedical Biology and Electron Microscopy Centre, Medical Faculty, University of Rostock, D-18057 Rostock, Germany (M.F.).
authors.forename: Marcus
authors.identifier: http://orcid.org/0000-0002-2517-4440
authors.initials: M
authors.lastname: Frank
authors.affiliation: Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.);Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., W.R.H.);Plant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.); andMedical Biology and Electron Microscopy Centre, Medical Faculty, University of Rostock, D-18057 Rostock, Germany (M.F.).
authors.forename: Wolfgang R
authors.initials: WR
authors.lastname: Hess
authors.affiliation: Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.);Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., W.R.H.);Plant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.); andMedical Biology and Electron Microscopy Centre, Medical Faculty, University of Rostock, D-18057 Rostock, Germany (M.F.).
authors.forename: Martin
authors.initials: M
authors.lastname: Hagemann
authors.affiliation: Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.);Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., W.R.H.);Plant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.); andMedical Biology and Electron Microscopy Centre, Medical Faculty, University of Rostock, D-18057 Rostock, Germany (M.F.) kopka@mpimp-golm.mpg.de.
authors.forename: Joachim
authors.identifier: http://orcid.org/0000-0001-9675-4883
authors.initials: J
authors.lastname: Kopka
mesh_terms: D000064:Acclimatization; D001639:Bicarbonates / Q000378:metabolism*; D001692:Biological Transport; D002245:Carbon Dioxide / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D055442:Metabolome; D009154:Mutation; D009584:Nitrogen / Q000378:metabolism; D009876:Operon / Q000235:genetics; D010788:Photosynthesis; D016372:RNA, Antisense / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D046939:Synechocystis / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D059467:Transcriptome
chemical_list: D001639:Bicarbonates; D016372:RNA, Antisense; D034741:RNA, Small Interfering; D002245:Carbon Dioxide; D009584:Nitrogen