Integrative Approach to Energy, Carbon, and Redox Metabolism in the Cyanobacterium Synechocystis sp. PCC 6803. (Final Report for November 15, 2003-November 14, 2004.)
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The main objectives for this year (adjusted to reflect a new, public domain, setting of the Project research team) were: Aim 1. To develop, test, and deploy a new open source system, the SEED, for integrating community-based annotation, and comparative analysis of all publicly available microbial genomes. Develop a comprehensive genomic database byintegrating within SEED all publicly available complete and nearly complete genome sequences with special emphasis on genomes of cyanobacteria, phototrophic eukaryotes, and anoxygenic phototrophic bacteria - invaluable for comparative genomic studies of energy and carbon metabolism in Synechocystis sp. PCC 6803. Aim 2. To develop the SEED's biological content in the form of a collection of encoded Subsystems largely covering the conserved cellular machinery in prokaryotes (and central metabolic machinery in eukaryotes). Aim 3. To develop, utilizing core SEED technology, the CyanoSEED - a specialized WEB portal for community-based annotation, and comparative analysis of all publicly available cyanobacterial genomes. Encode the set of additional subsystems representing key metabolic transformations in cyanobacteria and other photoautotrophs. We envisioned this resource as complementary to other public access databases for comparative genomic analysis currently available to the cyanobacterial research community. Aim 4. Perform in-depth analysis of several subsystems covering energy, carbon, and redox metabolism in the Synechocystis sp. PCC 6803 and all other cyanobacteria with available genome sequences. Reveal inconsistencies and gaps in the current knowledge of these subsystems. Use functional and genome context analysis tools in CyanoSEED to predict, whenever possible, candidate genes for inferred functional roles. To disseminate freely these conjectures and predictions by publishing them on CyanoSEED (http://cyanoseed.thefig.info/) and the Subsystems Forum (http://brucella.uchicago. edu/SubsystemForum/) in orderto facilitate experimental analysis by our collaborator on this Project and by other experimentalists working in various field of cyanobacterialphysiology and biotechnology.
Integrative Approach to Energy, Carbon, and Redox Metabolism in the Cyanobacterium Synechocystis sp. PCC 6803. (Final Report for November 15, 2003-November 14, 2004.)