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Abstract
Freshwater Synechocystis sp. PCC 6803 has been considered to be a platform for the production of the next generation of biofuels and is used as a model organism in various fields. Various genomics, transcriptomics, metabolomics, and proteomics studies have been performed on this strain, whereas marine Synechocystis sp. PCC 7338 has not been widely studied despite its wide distribution. This study analyzed the proteome profiles of two Synechocystis strains using a liquid chromatography–tandem mass spectrometry-based bottom-up proteomic approach. Proteomic profiling of Synechocystis sp. PCC 7338 was performed for the first time with a data-dependent acquisition method, revealing 18,779 unique peptides and 1794 protein groups. A data-independent acquisition method was carried out for the comparative quantitation of Synechocystis sp. PCC 6803 and 7338. Among 2049 quantified proteins, 185 up- and 211 down-regulated proteins were defined in Synechocystis sp. PCC 7338. Some characteristics in the proteome of Synechocystis sp. PCC 7338 were revealed, such as its adaptation to living conditions, including the down-regulation of some photosynthesis proteins, the up-regulation of kdpB, and the use of osmolyte glycine as a substrate in C1 metabolism for the regulation of carbon flow. This study will facilitate further studies on Synechocystis 7338 to define in depth the proteomic differences between it and other Synechocystis strains.
Highlights
Cyanobacteria, the only prokaryotes that perform oxygenic photosynthesis, have been considered as an attractive source for the direct production of chemicals and bioenergy from carbon dioxide (CO2) [1,2,3,4,5]
To increase peptide and protein identification in dependent acquisition (DDA), a chromatographic separation following the pre-fractionation of high pH reverse-phase (RP) fractionation and low pH RP LC was utilized since it allows the deep profiling of the proteomes and its effectiveness had been previously reported [69,70]
The global proteomic profiling of Synechocystis 7338 was conducted for the first time, whereas Synechocystis 6803 was used as a reference
Summary
Cyanobacteria, the only prokaryotes that perform oxygenic photosynthesis, have been considered as an attractive source for the direct production of chemicals and bioenergy from carbon dioxide (CO2) [1,2,3,4,5]. The gene functions and transformation mechanisms of Synechocystis have been studied at the genome level after the genome of Synechocystis 6803 was fully sequenced in 1996 [19] It produces various commodity chemicals such as ethanol, alkanes, fatty alcohol, fatty acids, ethylene, isoprene, and lactic acid [20,21,22,23]. PCC 7338 (hereafter, Synechocystis 7338) is an alternative organism that has the potential to be used in various fields. It was first isolated in 1970, only a few studies have been performed on this marine strain [24]. The study revealed metabolic differences of the marine strain under long-term exposure to salinity [27]
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