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Cyanothece sp and Synechocystis sp Comparison

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Reconstruction and Comparison of the Metabolic Potential of Cynobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

  • SITI HARYANI BINTI ANUAR

Problem Background

Cyanobacteria are prokaryotic cell which do not have nucleus and lack some organelles. They also unicellular and reproduce or divide by binary fission. They habitats are common in lakes, ponds, springs, wetlands, streams, rivers and also in soil or on rock. Cyanobacteria have highly organized system of internal membrane which functions in photosynthesis. Their capability of photosynthetic, ease of genetic modification and short life cycle are advantages over other microbes in the industrial production of valuable bio product and also as platform for harvesting solar energy [1]. Most cyanobacteria are photoautotrophic organisms where energy comes from light and carbon from carbon dioxide, while some are also photoheterotrophic, which means they use light to generate energy but they must obtain carbon in organic form. They also play a major role in the nitrogen cycle, carbon sequestration, and oxygen production of many aquatic environments.

Cyanobacteria are endowed with high photosynthetic efficiencies and diverse metabolic capabilities that confer the ability to convert solar energy into a variety of biofuel and their precursors [1]. Those metabolic capabilities can refer as the complete set of chemical reactions that occur in living organisms in order to maintain its life. So, what we need here is we expanded upon existing model to develop genome scale model for cyanobacteria metabolism. A genome-scale metabolic network of chemical reactions that take place inside a living organism is primarily reconstructed from the information that is present in its genome and the literature and involves steps such as functional annotation of the genome, identification of the associated reactions and determination of their stoichiometry, assignment of localization, determination of the biomass composition, estimation of energy requirements, and definition of model constraints [2]. This information can be integrated into a stoichiometric model of metabolism that can be used for detailed analysis of the metabolic potential of the organism using constraint-based modeling approaches and hence is valuable in understanding its metabolic capabilities.

For cyanobacteria, there are two phylogenetically related cyanobacteria species, which are Cyanothece sp. ATTCC 51142 and Synechocystis sp. PCC 6803. In this paper, we want to assemble, update and compare genome scale model for those two phylogenetically related cyanobacteria species. Cyanothece sp. ATTCC 51142 is one of the most potent diazotrophs characterized and the first to be completely sequence [3] which can fix atmospheric nitrogen and also accommodate the biochemically incompatible processes of photosynthesis and nitrogen fixation [4]. While, Synechocystis sp. PCC 6803 with complete sequenced genome is first photosynthetic organism [5], that probably the most extensively studied model organism for photosynthetic organism [6]. Both of this two species are closely related and share many characteristics.

As we know, Synechocystis 6803 always has been target for metabolic model reconstruction for several times which is focused on only central metabolism and they always involved in genetic manipulation. In contrast to Cyanothece 51142, the genetic tools are not currently available, thus prevent its wide use as bio-production strain. Therefore, its requires high quality metabolic models that integrate all recent developments supplement with additional literature review evidence and highlight their similarities and differences for both organisms[1]. Comprehensive genome-wide metabolic reconstructions include the complete inventory of metabolic transformations of a given cyanobacteria system [1]. Comparison of the metabolic capabilities of Cyanothece 51142 and Synechocystis 6803 derived from their corresponding genome-scale models will provide valuable insights into their niche biological functions and also open up new avenues for economical biofuel production [1].

Problem Statement

Cyanobacteria are the importance group of photoautotrophic organism that can synthesize valuable bio-products by harnessing solar energy. There are valuable two phylogenetic Cyanobacteria species which are Cyanothece sp. ATTC 5114 and Synechocystis sp PCC 6803. Synechocystis 6803 always has been target for metabolic model reconstruction for several times which is focused on only central metabolism and they always involved in genetic manipulation. In contrast to Cyanothece 51142, the genetic tools are not currently available, thus prevent its wide use as bio-production strain. Therefore, its requires high quality metabolic models that integrate all recent developments supplement with additional literature review evidence and highlight their similarities and differences for both organisms [1]. Genome-scale model is use to compare the metabolic pathway capabilities of Cyanothece 51142 and Synechocystis 6803 which provide valuable insights into niche functions and also open up new avenues for economical biofuel production. By introduces high-quality genome-scale model for Cyanothece sp. ATTCC 51142 and Synechocystis sp. PCC 6803, it will integrate all recent developments and improved understanding of the metabolic pathway because genome-scale model (GSM) contain gene to protein to reaction association (GPRs) along with stoichiometric representation of all possible biotransformation known to occur in organism combined with set of appropriate regulatory constraints on each reaction flux. Comprehensive genome-wide metabolic reconstructions include the complete inventory of metabolic transformations of a given cyanobacteria system. Comparison of the metabolic capabilities of Cyanothece 51142 and Synechocystis 6803 derived from their corresponding genome-scale models will provide valuable insights into their niche biological functions and also open up new avenues for economical biofuel production [1].

Research Goals and Objective

The goal of this research is to assemble, update and compare genome scale model of iCyt773 and iSyn731 for two phylogentically related Cyanobacteria species which are Cyanothece sp. ATTCC 51142 and Synechocystis sp. PCC 6803

Several objectives have been established for this research in order to achieve the goal that mentioned in the above, they are:

  1. To analyze the metabolic potential of Cyanothece sp. ATTCC 51142 and Synechocystis sp. PCC 6803.
  2. To reconstruct Genome-Scale Model (GMS) and compare the metabolic potential of Cyanothece sp. ATTCC 51142 (iCyt773) and Synechocystis sp. PCC 6803 (iSyn731) by using Flux balance analysis (FBA)
  3. To evaluate the similarities and differences and unique reaction and metabolites between iCyt773 and iSyn731.

Research Scope

Several scopes haven been identified for this research, they are:

  1. Flux balance analysis (FBA) is employed in both model validation and model testing phase.
  2. The dataset that using in this research are SBML file of Synechocystis iSyn731 model and SBML file of Cyanothece 51142 iCyt773 model.
  3. The dataset format is in System Biology Markup Language (SBML) format.
  4. CPLEX solver is use in GAMS environment to implementing the GapFind and GapFill and solving the aforementioned models.

Research significant

Research Planning

[1] 2012 reconstruction and comparison

[2] 2012, Gino J. E. Baart, Dirk E. Martens

[3] Welsh EA, Liberton M, Stockel J, Loh T, Elvitigala T, et al. (2008)

[4] Zehr JP, Church MJ, Moisander PH (2005)

[5] Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, et al. (1996)

[6] Knoop H, Zilliges Y, Lockau W, Steuer R (2010)


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