title: Development of a Quantitative SRM-Based Proteomics Method to Study Iron Metabolism of Synechocystis sp. PCC 6803.
abstract: The cyanobacterium Synechocystis sp. PCC 6803 (S. 6803) is a well-established model species in oxygenic photosynthesis research and a potential host for biotechnological applications. Despite recent advances in genome sequencing and microarray techniques applied in systems biology, quantitative proteomics approaches with corresponding accuracy and depth are scarce for S. 6803. In this study, we developed a protocol to screen changes in the expression of 106 proteins representing central metabolic pathways in S. 6803 with a targeted mass spectrometry method, selected reaction monitoring (SRM). We evaluated the response to the exposure of both short- and long-term iron deprivation. The experimental setup enabled the relative quantification of 96 proteins, with 87 and 92 proteins showing adjusted p-values <0.01 under short- and long-term iron deficiency, respectively. The high sensitivity of the SRM method for S. 6803 was demonstrated by providing quantitative data for altogether 64 proteins that previously could not be detected with the classical data-dependent MS approach under similar conditions. This highlights the effectiveness of SRM for quantification and extends the analytical capability to low-abundance proteins in unfractionated samples of S. 6803. The SRM assays and other generated information are now publicly available via PASSEL and Panorama.
authors.affiliation: Molecular Plant Biology, Department of Biochemistry, University of Turku , FI-20014 Turku, Finland.
authors.forename: Linda
authors.initials: L
authors.lastname: Vuorijoki
authors.affiliation: Molecular Plant Biology, Department of Biochemistry, University of Turku , FI-20014 Turku, Finland.
authors.forename: Janne
authors.initials: J
authors.lastname: Isojärvi
authors.affiliation: Molecular Plant Biology, Department of Biochemistry, University of Turku , FI-20014 Turku, Finland.
authors.forename: Pauli
authors.initials: P
authors.lastname: Kallio
authors.affiliation: Turku Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University , FI-20014 Turku, Finland.
authors.forename: Petri
authors.initials: P
authors.lastname: Kouvonen
authors.affiliation: Molecular Plant Biology, Department of Biochemistry, University of Turku , FI-20014 Turku, Finland.
authors.forename: Eva-Mari
authors.initials: EM
authors.lastname: Aro
authors.affiliation: Turku Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University , FI-20014 Turku, Finland.|Van't Hoff Institute for Molecular Sciences, University of Amsterdam , 1018 WV Amsterdam, The Netherlands.
authors.forename: Garry L
authors.initials: GL
authors.lastname: Corthals
authors.affiliation: Department of Life Sciences, Imperial College London , Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom.
authors.forename: Patrik R
authors.initials: PR
authors.lastname: Jones
authors.affiliation: Molecular Plant Biology, Department of Biochemistry, University of Turku , FI-20014 Turku, Finland.|Turku Proteomics Facility, Centre for Biotechnology, University of Turku and Åbo Akademi University , FI-20014 Turku, Finland.
authors.forename: Dorota
authors.initials: D
authors.lastname: Muth-Pawlak
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D002851:Chromatography, High Pressure Liquid; D007501:Iron / Q000378:metabolism*; D010788:Photosynthesis; D020543:Proteome / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D046939:Synechocystis / Q000378:metabolism*; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins; D020543:Proteome; D007501:Iron
keywords: Synechocystis sp. PCC 6803; cyanobacteria; iron deprivation; metabolism; quantitative proteomics; selected reaction monitoring (SRM)